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CM403 Wont Run Standalone but Works in Debug and Release

I've been using the CM403 and had no issues with it running standalone until i added JAM byte code player code to program a MAX 10 FPGA. Everything works when running in debug and in release but when i reset the power it seems to get held up. 

I have a hunch it has to do with Flash because I'm storing a large FPGA image there but I'm not certain. I've been referring to  but still not having luck. It's been 2 weeks and I've made no progress... Any help would be greatly appreciated.