[kamocat]

QCEliteTeam648,
This is complex code. At the moment I can understand subsections and groups of functions, but I don't understand "the big picture".
The issue with encoders is almost certainly an interaction between software components that, by themselves, function correctly. While it does have something to do with your code to test the encoders, there are other parts of the code that are contributing to the issue. These sorts of problems are notoriously hard to troubleshoot and diagnose. The difficulty is amplified by hard-to-read code (especially large block diagrams).

I think the best way we can help you is by providing suggestions for ALL of your code in a process termed peer review. Suggestions are usually given in three categories: efficiency, cleanliness, and documentation.

Would you like to open up the entire project to peer review?