Clutch problem

[straightdrive]

So for a little background, My 05 f250 has about 134k on it. Its got 4x4, the 6.0, along with a gooseneck, and the manual trans. I recently bought the truck, and it worked fine when i bought it and for the past two months.

Now it has started acting up. Coincidentally it started right after my installation of a SCT tuner. When it downloaded the program (generic "Performance") onto the truck the tuner displayed that it was tuning the trans, what does this mean???? I knew the autos are computerized, but is there a computer controling something within the manuals?
Anyways im having a problem with my clutch, sometimes it will stick when I put the clutch in. It will pop back out if I pull it with the top of my foot, but this doesn't make the truck very driveable. This usually happens if I get into the throttle. I'll start then go to shift and the clutch will work normally for the first to second gear change. I'll keep on it and go for the second to third shift, by this point the clutch pedal stroke will become shorted with every shift, until it just sticks. This is also moving the point where the clutch would begin to bite, which when I star off, is inconvienent at the least.
I have returned the truck to the stock programming, but I have not been able to drive it with the stock programming back on it, to see if the tuning caused this.