Common problems I've found while playing around with the creation of Windows installers is that if you break the uninstaller functionality it's very difficult to uninstall at all.
There are a couple of ways to attempt to repair, this
1. Force overwrite of the installer with a known good installer and then uninstall.
2. Repair the installer with a known good installer (Control Panel->Add/Remove Programs, locate you Applications installer and select "Click here for support Information", then select Repair from the resultant dialog, now point to a new location of a good installer)
3. Use a tool name MsiZip.exe, it's available with the
4. A Windows Installer Cleanup Utility.
The windows installer keeps a list in the OS of files installed by the installer, if you cannot uninstall because windows thinks one of these files is being used then try option 1 above.