Rough Shifting of 6-Speed transmission

I have a 2008 6-Speed Tacoma. The clutch in my truck is very touchy. Even when I try changing gears as smoothly as I can, it often shifts roughly. Sometime back, I unhooked my battery cables when I was doing something to my truck. When I drove my truck after that it shifted smooth as the day I drove it off the lot. It will do fine for a week or so and then seems to gradually start shifting rough again. Every time I unhook the battery cables and hook them back, it shifts great. I was wondering if someone could tell me what could be wrong.

 

I have the same issue with my 08 sport trd. Its 1st to 2nd for me. All the other gears are fine. Clutch is fine too.