I have a hard time seeing how this could have anything to do with SVN. Are you sure you didn't have a conflict after doing an update? Ending up with a bunch of ">>>>> mine" or similar lines in it from a conflict would certainly cause issues. Otherwise, it's still just going to be a PDE file, the contents of the file don't change just because they're checked into SVN. I'd try opening the file in notepad and looking for the conflict headers.
Yeah, it's SVN based, no others are affected. But I'm happy to put this down to quirks mode. This affects two sketches (one of which has been reproduced on another pc), but other sketches are unaffected.
When the Arduino IDE opens up a sketch, it tries to do "things" with pretty much all the files in the directory, and it can get confused if it finds files that it doesn't recognize (it gets MORE confused when it THINKS that it recognizes a file, but is wrong...)
Unplug Bluetooth adapter (worked for me).
Close/Disable Bluetooth software, e.g. Bluesoleil.exe and btntservice.exe
Delete preferences.txt
Windows 7: C:\Users<user>\AppData\Roaming\Arduino\preferences.txt
Windows XP: C:\Documents and Settings<user>\Application Data\Arduino\preferences.txt.