How desperate are you to fix this? Searching the web this problem for a very few people has been going on since at least 2009. I was not able to find any definitive resolutions but as you say the problem doesn't happen with a new user account but does happen with a new library your account does give us some place to look. However the process is going to be a long one (unless you get lucky) .
So if you're interested in a nutshell here's what you do:
First thing i you haven't already run Font Book and cleaned up your fonts do that first. Re-boot machine and run Aperture. Is it fixed? If so I'm a genius 🙂 (who should have thought of that a while back) If not continue.
Because it doesn't happen to a new user it would indicate a problem somewhere in your environment. The most likely place is somewhere in your preferences. Of course which one there a lot of files in the Preferences folder. You could make some logical guesses and remove those but that could take a really long time. So fist step is:
Remove ALL the files from your Preferences folder (remember we're troubleshooting so hang in there)
Now with the Preferences folder empty re-boot the machine and log in. You'll be in a clean environment as if you just installed the OS. Now:
Run Aperture and (hopefully) the tool tips are OK
If you wanted to recreate everything from scratch you could stop here and as you run programs just recreate their preferences. But if you want to figure out what happened (or have to many preferences to recreate) continue.
- Add back half the files from the original Preferences. Make sure you keep track of the files you're adding back
- Re-boot, run Aperture check tool tips.
If they still work add in the second half, repeat as above (re-boot, run Aperture, results?)
Hopefully they stopped working then its a question of removing half the just added files and seeing if the tool tips work, etc. I think you can see the general plan here. You're trying to get it down to that one preferences file.
Now there are two ways this can fail (only two?!) One is if when you empty the Preference folder the first time and run Aperture the tool tips are still messed up. The other is if the problem is caused by an interaction between two (or more) preferences files. Lets be optimistic for the time being and assume the problem is caused by a single preference file in your Preferences folder.
let me know if you decide to do this. Really would love to know what's casuing it.
regards