I've created a working configuration in ACE and tested it on the evaluation board. I converted it to a bin file using the python script, which works although it gives a number of warning messages:
Missing data for Register: 0x301. Using Default Data. Missing data for Register: 0x302. Using Default Data. Missing data for Register: 0x303. Using Default Data. Missing data for Register: 0x1029. Using Default Data. Missing data for Register: 0x10c0. Using Default Data. Missing data for Register: 0x10c1. Using Default Data. Missing data for Register: 0x10c2. Using Default Data. Missing data for Register: 0x10c3. Using Default Data. Missing data for Register: 0x10c4. Using Default Data. Missing data for Register: 0x10c5. Using Default Data. Missing data for Register: 0x10c6. Using Default Data. Missing data for Register: 0x10c7. Using Default Data. Missing data for Register: 0x10c8. Using Default Data. Missing data for Register: 0x10c9. Using Default Data. Missing data for Register: 0x10ca. Using Default Data. Missing data for Register: 0x10cb. Using Default Data. Missing data for Register: 0x10cc. Using Default Data. Missing data for Register: 0x10cd. Using Default Data. Missing data for Register: 0x10cf. Using Default Data. Missing data for Register: 0x10d0. Using Default Data. Missing data for Register: 0x10d1. Using Default Data. Requested Register: 0x1429 does not exist. Using Data = 0x00. Missing data for Register: 0x14c0. Using Default Data. Missing data for Register: 0x14c1. Using Default Data. Missing data for Register: 0x14c2. Using Default Data. Missing data for Register: 0x14c3. Using Default Data. Missing data for Register: 0x14c4. Using Default Data. Missing data for Register: 0x14c5. Using Default Data. Missing data for Register: 0x14c6. Using Default Data. Missing data for Register: 0x14c7. Using Default Data. Missing data for Register: 0x14c8. Using Default Data. Missing data for Register: 0x14c9. Using Default Data. Requested Register: 0x14ca does not exist. Using Data = 0x00. Requested Register: 0x14cb does not exist. Using Data = 0x00. Requested Register: 0x14cc does not exist. Using Data = 0x00. Requested Register: 0x14cd does not exist. Using Data = 0x00. Missing data for Register: 0x14cf. Using Default Data. Missing data for Register: 0x14d0. Using Default Data. Requested Register: 0x14d1 does not exist. Using Data = 0x00. Requested Register: 0x14d5 does not exist. Using Data = 0x00. Requested Register: 0x14d9 does not exist. Using Data = 0x00. Requested Register: 0x2015 does not exist. Using Data = 0x00. Requested Register: 0x2204 does not exist. Using Data = 0x00. Missing data for Register: 0x2800. Using Default Data. Missing data for Register: 0x2801. Using Default Data. Missing data for Register: 0x2802. Using Default Data. Missing data for Register: 0x2803. Using Default Data. Missing data for Register: 0x2804. Using Default Data. Missing data for Register: 0x2805. Using Default Data. Missing data for Register: 0x2806. Using Default Data. Missing data for Register: 0x2807. Using Default Data. Missing data for Register: 0x2808. Using Default Data. Missing data for Register: 0x2809. Using Default Data. Missing data for Register: 0x280a. Using Default Data. Missing data for Register: 0x280b. Using Default Data. Missing data for Register: 0x280c. Using Default Data. Missing data for Register: 0x280d. Using Default Data. Missing data for Register: 0x280e. Using Default Data. Missing data for Register: 0x280f. Using Default Data. Missing data for Register: 0x2810. Using Default Data. Missing data for Register: 0x2811. Using Default Data. Missing data for Register: 0x2812. Using Default Data. Missing data for Register: 0x2813. Using Default Data. Missing data for Register: 0x2814. Using Default Data. Missing data for Register: 0x2815. Using Default Data. Missing data for Register: 0x2816. Using Default Data. Missing data for Register: 0x2817. Using Default Data. Missing data for Register: 0x2818. Using Default Data. Missing data for Register: 0x2819. Using Default Data. Missing data for Register: 0x281a. Using Default Data. Missing data for Register: 0x281b. Using Default Data. Missing data for Register: 0x281c. Using Default Data. Missing data for Register: 0x281d. Using Default Data. Missing data for Register: 0x281e. Using Default Data. Missing data for Register: 0x2840. Using Default Data. Missing data for Register: 0x2841. Using Default Data. Missing data for Register: 0x2842. Using Default Data. Missing data for Register: 0x2843. Using Default Data. Missing data for Register: 0x2844. Using Default Data. Missing data for Register: 0x2845. Using Default Data. Missing data for Register: 0x2846. Using Default Data. Missing data for Register: 0x2847. Using Default Data. Missing data for Register: 0x2848. Using Default Data. Missing data for Register: 0x2849. Using Default Data. Missing data for Register: 0x284a. Using Default Data. Missing data for Register: 0x284b. Using Default Data. Missing data for Register: 0x284c. Using Default Data. Missing data for Register: 0x284d. Using Default Data. Missing data for Register: 0x284e. Using Default Data. Missing data for Register: 0x284f. Using Default Data. Missing data for Register: 0x2850. Using Default Data. Missing data for Register: 0x2851. Using Default Data. Missing data for Register: 0x2852. Using Default Data. Missing data for Register: 0x2853. Using Default Data. Missing data for Register: 0x2854. Using Default Data. Missing data for Register: 0x2855. Using Default Data. Missing data for Register: 0x2856. Using Default Data. Missing data for Register: 0x2857. Using Default Data. Missing data for Register: 0x2858. Using Default Data. Missing data for Register: 0x2859. Using Default Data. Missing data for Register: 0x285a. Using Default Data. Missing data for Register: 0x285b. Using Default Data. Missing data for Register: 0x285c. Using Default Data. Missing data for Register: 0x285d. Using Default Data. Missing data for Register: 0x285e. Using Default Data. Missing data for Register: 0x2a00. Using Default Data. Missing data for Register: 0x2a01. Using Default Data. Missing data for Register: 0x2a02. Using Default Data. Missing data for Register: 0x2a03. Using Default Data. Missing data for Register: 0x2a04. Using Default Data. Missing data for Register: 0x2a05. Using Default Data. Missing data for Register: 0x2a06. Using Default Data. Missing data for Register: 0x2a07. Using Default Data. Missing data for Register: 0x2a08. Using Default Data. Missing data for Register: 0x2a09. Using Default Data. Missing data for Register: 0x2a0a. Using Default Data. Missing data for Register: 0x2a0b. Using Default Data. Missing data for Register: 0x2a0c. Using Default Data. Missing data for Register: 0x2a0d. Using Default Data. Missing data for Register: 0x2a0e. Using Default Data. Missing data for Register: 0x2a0f. Using Default Data. Missing data for Register: 0x2a10. Using Default Data. Missing data for Register: 0x2a11. Using Default Data. Missing data for Register: 0x2a12. Using Default Data. Missing data for Register: 0x2a13. Using Default Data. Missing data for Register: 0x2a14. Using Default Data. Missing data for Register: 0x2a15. Using Default Data. Missing data for Register: 0x2a16. Using Default Data. Missing data for Register: 0x2a17. Using Default Data. Checksum is: 0xb4206fd
I removed the EEPROM and put it in an external programmer and verified that the bytes were copied. Next I put the EEPROM back into the evaluation board, and set the M3 jumper as described in the wiki:
This lights up a red LED and puts TP603 to 1.8V, but on power up the PLL has no output. If I power up, then remove the M3 jumper, I can read back the registers in ACE, which are default.
I'm not sure what else to try. Perhaps I have made the bin file incorrectly?