I can’t think of any app that employs online updates, that hasn’t had major troubles with them. Java is the #1 candidate, but flash and acrobat are definitely high on the list. I recommend you to only install these toys from pre-downloaded full installers (not the type that download the files from the internet to install them, the big one that needs no net connection to work), and after installing them, immediately disable the online updater. Doing so will avoid troubles like this one. Don’t even get me started on the f***ing mess that the java updaters make on your machine…
Another classic misbehaviour is the fact that these tools rarely uninstall correctly (read: completely) and instead leave behind files and, most notably, registry entries. To compound the matter, the installers tend not to overwrite existing settings with ‘known-good, out-of-the-box’ settings, instead preferring your existing (in this case, broken) settings. As such, while uninstall/reinstall can be educational, it doesn’t always fix stuff. Damn.
Some software shops even go to the extent of supplying a “real” uninstaller, which actually does a full (read: complete) uninstall, and has to be separately downloaded (Symantec comes to mind). If the software you’re having troubles with doesn’t have such a tool provided (or you can’t find it - eg, the symantec uninstaller used to be highly secret and not available unless you held an enterprise license worth several tens of thousands of dollars) then you can go the manual route - searching the registry (use Registrar Lite, not regedit.exe - hot tip!!) and removing the entries as needed, and manually deleting program files/common files/etc. Beware that if you do this stuff you might just trash your PC.
If the preventative measures I’ve suggested are too late (like this one) or the manual cleanups don’t work or are too risky, then your only real option is to file bugs with the project in question. If you’re an advanced user, you will probably be alone in reporting the issue, so it will look minor, and you can expect to be largely ignored, then spend weeks on testing to prove to the devs that the problem really is with their software, then be asked to completely reinstall your system to a reformatted drive, which will fix the problem and they’ll probably blame some other app, then you’ll be largely ignored for some time afterwards and maybe get a fix in the next minor release, if you’re lucky…
Don’t you wish all software was written by TK? I sure as f*** do!!!
In the meantime… try the ‘manual uninstall’, and turn off your updates this time 