Sorry for my dumb answer but have you tried a new pad? Battery in your disconnecting one may be worn out and your controller simply runs out of juice quickly when vibrations are switched on... Resulting in disconnects... How old is your pad? Have you seen a PS3 message poping up before your pad drops out?

You're using keyboard and mouse? Is it possible that the DS3 controller is just timing out?

Nope, because sometimes it will happen right after I push the PS button and before I can even get my hand back on the mouse it is at the please reconnect controller screen. This is also with the controller plugged into the PS3. It is honestly the weirdest of all the bugs I have found in DUST so far.

I have to say, Kal is probably right ... I think the _weirdest_ one in my book is probably the empty-hands spawn bug from a few weeks back. That was fun. Made it to a supply depot, but changing suits, of course, didn't help, so I just ran at red dots until one of 'em gave me a "free" trip back to the MCC. Took rather longer than I expected, actually... I don't know if I was just moving oddly on his screen, or if he was sufficiently surprised to see someone running straight at him with no weapons, equipment, or anything in his hands at all.

Whatever. Back to your controller's annoying behavior. Um. So, yeah. I think the only advice I can give is to shut off the vibration function. If the vibration is actually the cause, and not merely coincidental, it should take care of the problem.

[PS button] -> Settings -> Accessory Settings -> Controller Vibration Function
(not that I think you don't know where the setting is; you never know, some neophyte might be reading this looking for help with the same or a similar issue)

(I'm assuming that when you said you had this issue on 3 different PS3s, that implies 3 different DS3 controllers, too. Oh! hey, actually - did you use different KBDs and Meese, too? It seems unlikely, but I'd guess it's ~possible~ that there might be some signal being sent by This Company's keyboard that isn't sent by That Company's one that might cause this weirdness. I dunno, but if you did tote your keyboard and mouse over to a bud's place to test it, maybe try with different ones.)

Anyway, good luck, dude, and good hunting! (both of Red Dots and Bugs!)