This is solved. If anyone experiences the same issues, this is what worked for me.
- Clear all cache (EdpSuperluminal, APC etc.)
- Remove Zend library
- Run your application without Zend library (giving loads of errors of course, but this seemed crucial to me to make it work)
- Re-install Zend library
- Run your application again
I installed 2.1.5dev and it fixed the issue. Wanted to make sure whether it was a bug or not so tried again with 2.1.4 and the issue was still fixed. So this is my conclusion. Cache can be a weird thing.
Edit Jumped to (the wrong) conclusions too soon. Fired up Zend Studio 10 and now it bugs again. I think Zend Studio 10 is reverting some files (not all since Query route did got marked as deprecated). Still, consider this solved, just need to find a way to tell Zend Studio 10 to use 2.1.4. Thanks!