Well, it was a dumb reply from a not so detailed question. We really need code and expected result and actual result. Even then we might not call into question the docs available and code that works.
Coding is a lesson in humility. You
really question your own code first - even when you're experienced. And then when you're really experienced and there can be no error anywhere, you really question your own code before anything. And then when you've found the problem and reduced it to a single instruction that can't possibly fail, you still question your own code before anything. This is the lesson.
Here's the answer I should have written, perhaps.
Blitter corruption (whatever that is, we don't know cos you don't show), is caused by your code because WinUAE can't cause it.
But here's the thing: this might be a false statement, and I don't write those.
Because it IS possible that if you took a correct Blitter init and completely jumbled the order of statements, you could (maybe) provoke WinUAE into failing. It's
extremely unlikely, but possible.
Coppershade has only 100% accurate descriptions and only 100% working code, or it's not on Coppershade. This is how tough it is to get published there, and I'm my own author! 
So if you accept that WinUAE didn't corrupt your blits, and my blitwait didn't, and you show some code, and wrong result, and expected result, you will get excellent help in this, the best Amiga forum.