That is strange!?!?!

Verify that the problem extension is in the same keymap as the others as well. Also, verify that lines 3 and 4 are indeed lines 3 and 4. Maybe they have moved into the alternate keymap which only has 2 call keys.

If all seems normal there, you may want to delete the extension and re-create it if it's some sort of glitch. Make sure of course to put them back into any hunt group, page zone, extension list, keymap, etc.