king3pj :
I have only had Far Cry 4 for a few weeks. I got it when it was the Amazon deal of the day for $30. That being said, I have only played the game with my wireless 360 controller and usb dongle. I have never experienced any of the problems people are reporting here.
I have an FX 6300, GTX 970, and run Windows 8.1. From the responses here, it seems like the problem only seems to be affecting Windows 7 users. I have never had any third party programs that allow you to use the 360 controller on games that don't have native support though. That could be the issue as well.
The amount of time I spent trying to get it working is absolutely insane,I did literally everything short of a full clean windows 7 install.Tried cracked game exe files & updates from all kinds of dubious sources as a last resort.
I do use pinnacle game profiler,but uninstalled completely ,made no difference,toatlly removed all my HID drivers & devices,dropped to a wired keyboard & mouse instead of my logitech unified wireless stuff.still no cigar
The prebuild I did for someone ,I installed literally everything I had on my own pc,including logitech wireless drivers etc,worked first time with pad without a problem.
I was going to try swapping cards out with my 280x,but was offered a windows 8 upgrade key cheap,used it & the game worked instantly from then on,so had no need.
There are reports of the game not working with peoples wireless keyboards & mice (far worse then the 360 pad issue - to all intents that makes the game unfit for purpose completely) - all of these reports are on windows 7 ,no such issues on windows 8/8.1 at all.