I had something similar.

In my case, I had turned on FTL on some of the DPS Keymaps.
Check that you have "Use FTL Modifiers" set to Default on every other keymap.

The only three that want it set to "On" are:
-- FTL Assist Me, FTL Target Me, and FTL Follow Me.

If that is not the case, you could try to link your config via Pastebin.com
Open up ISBoxer Toolkit, right click on IS Boxer in the top pane, and copy your config.
Go to www.pastebin.com and paste it there.
I would search for your B.Net email, and edit it out of the file.
Set it to save for a month, and post the link here.

You can also go to the IS Boxer IRC.
You'll get faster response there (it is a chat), then waiting here.
But either works.
The IRC is found at: http://www.lavishsoft.com/chat/isboxer.php