If anyone has the same problem and finds this then pay attention to the number of data points you are using for training.
I was using "to workspace blocks" with sample times of 0.001 to collect my training data, but they didn't collect at anything near the proper times, or time intervals. (intervals of 0.001 for 200s should obviously produce 200000 data poitnts, but i was collecting someting like 66667).
I switched to using scope blocks to collect my data instead, and now I have the correct data, and my gensim network responds identically to the network it was gensimed from (when using identical inputs).