How can I find what is interfering with CTRL+F?

I had the same problem on Linux Mint 13 and the same output on xev, namely Control_l + f was mapped to Control_l.

My solution: I remembered that I have xbindkeys running to enable some exotic buttons on my tablet pc.

By running xbindkeys-config and checking all key mappings defined for xbindkeys I found an entry that interfered with CTRL-F.

After deleting the offending mapping and saving the new settings, CTRL-F works again and correctly launches the search dialog in gedit, firefox, ...

I know it's not a perfect solution, but you can try to eliminate processes one by one to figure out which one do the mess, but first:

Create another user, and test it there to verify if it's a user-settings specific.

Change window manager to simplest possible (twm?) to see if it's a window manager specific.

Good luck.