Welcome to the community @NAR1. 
Make sure you are using the correct trainer. This is the one you should need: Borderlands Game of the Year Enhanced Cheats and Trainer for Steam. Not the regular Borderlands trainer.
Trainers do not touch the game in any way at all, they just inject values into your PC’s RAM. Frame drops are usually hardware-related, not software related.
For example, they can be caused by overheating, not meeting the minimum specs to run both the game and WeMod together, Windows fragmentation (when was the last time you defragmented your hard drive?), GPU bottlenecking, outdated drivers, etc.