If it works in Debug mode, then you need to make sure that the version Excel is loading when NOT in debug mode is actually the updated version (the one where you removed those lines of code in ThisAddin_Shutdown).
If that does not solve the problem, there's no way we can help you further, other than tell you how to go about trouble-shooting the problem. Obviously, it's something your add-in is doing, but there's no way to determine what that is for us, at this remove.
My suggestion would be to first create a new add-in, with "skeleton code" - no real functionality. Check that this works properly.
Then import the functionality of the problem add-in, bit-by-bit, in as small increments as possible. Test after each import until you isolate what's causing the problem.