It turns out it was all confusion.
There was some confusion between the comments in the code and the actual intent behind the code extraction. data_ml_functions/mlFunctions.py#L175 says "Custom generator that yields a vector containign the 4096-d CNN codes output by ResNet50 and metadata features...", which led to me generating codes that were supposed to be 4096-d, hence I edited the method to reflect that.
I think the comment is a vestige from the old baseline, and the intent was to create 2208-d codes + metadata. This was what was causing the error, and once I fixed that, it all worked.
Would you be able to push a commit that updates that comment?
Thanks! And sorry again for the confusion. Since I'm using make_parallel, I'm having to edit a lot of the code and got caught up in the comments instead of the single GPU model summery.