TX Path HDL inserts zeroes into IQ

Hello, 

I am porting some custom IP cores from ADI HDL and ADI Linux  releases 2016.2 to 2018.2

The actual IP Cores do not appear to be affected by this port (from viewing their change logs). However, when I insert them into the fmcomms2_bd.tcl file, the actual transmit data does not come out correctly. My working fmcomms2_bd file in 2016.2 did not have a FIFO on the transmit side, so I also took out the FIFO in 2018.2 Do I need to add it back in? I have attached a photo for reference. There are a few thing wrong with the transmitted waveform.

1) the modulated IQ waveform does not start at the beginng of the transmission

2) sectiions of true transmitted data of 8.3 usec are separated by sections of constant phase and amplitude. (My IP core takes bits and turns them into IQ so it is possible that these are 0s which were turned into 0 in BPSK, so it would still make sense to be putting out energy.)

3) even if these data sections were spliced together, the total transmit time is I think 4 times as long as it should be.

Any clues as to what could be happening here?