Since it sounds like you've tried many different potentional solutions, you'll probably have to do this the long methodical way now.
Create a new blank workbook. Then piece by piece copy your old workbook into it. Add a reference, write a little bit of code to test it. Ensure it compiles, ensure it runs. Add a sub or function, again, write a little test sub to run it, also ensure it compiles. Repeat this process slowly adding and testing everything.
You can speed this up a bit by first trying larger chunks, then when you find one that triggers the problem, remove it and break it into smaller peices for testing.
Either you will find the offender, or you'll have a new workbook that magically does not have the problem. The latter would be due to some sort of hidden corruption in the workbook file, probably in the binary vbproject part.
Welcome to the world of debugging without debuggers or other helpful tools to do the heavy lifting for you!