Does the problem persist if you save and restart the application? Save the painting to a new file using Save As just in case there is a problem.
It sounds like there is a modal operation in progress. Pressing Escape or Enter could end it (this may relate to transforming the layer contents, though I can't replicate the behaviour here).
If the problem does persist, we'll need to take a look at the file directly, let me know if the above doesn't help and we'll sort out getting the file from you to take a look at what's happening.