Thank you for the post.
The sample file provided is excellent and was submitted to Testing and Development as is. I can confirm this occurs both on Windows and Mac OS X.
One additional question to clarify: were any of the layout objects in the sample file copied from a converted file or another FileMaker Pro file?
I originally identified the issue while implementing in a Client's file (based upon Ocean) so I created a brand new file using Ocean with all new objects and it produced same behavior. I then created second file based upon Cool Gray (the one attached in the link) again with all new objects but I DID copy the two top-right buttons over from the newly created Ocean file.
I replicated the complexity exactly to the client file in case the issue was not with hover but rather with ExecuteSQL() or my implementation of the less-than-normal technique. The results remained consistent in all three files (all three created in 12.0v3 using FMPA on Windows XP SP3). I haven't tested the remaining themes, assuming that the button hover, layout layers and refresh would behave the same for all themes.
This issue has been added to the Known Bug List. Please post any comments about that entry here to keep the list "clean". A copy of the sample file was also added to the database entry for this bug report.