I had a similar problem that took me over 7-8 hours to rectify.
I had to get rid of TARGET and the Saitek software, then program the buttons via in-game controller option.
I just picked up Saitek Combat Pedals and Warthog HOTAS the other day, and the Saitek software installed something called Mad Katz, which I think totally f'ed up my DCS install. Mad Katz caused a "!" on my HD when I checked my device manager. So I got rid of it.
After deleting TARGET and Saitek software (and Mad Katz), had to do a Steam game integrity check, which found 90+ bad files. Steam dl and replaced the bad files and boom, I can now program my Warthog HOTAS and Saitek pedals via in-game menu.
Get rid of the Saitek software if installed, that will probably fix your sim. After you remove the software, do the integrity/file check.
Also, figured out I have various USB versions (my pc has 8-USB ports), and it matters which USB I use for the gear...which, from what I can tell, the one that functioned properly with my controller is any USB except 3.0 (I have 2.0, 3.0 and I think 1.1). Hard to tell, but may have 3.0 mixed up with the 1.1 version, as far as which ones work and which don't. Not sure how to determine which port is which, had to do trial and error for a bit.
Good luck!
DrDetroit