I know exactly what you mean!!! Personally, I have a big problem with standing up. I play guitar in my room all the time, so Im always sitting in front of the TV or computer. I have gotten so used to it, that when I stand up, its COMPLETELY different. It's easier to play sitting down because you have easier access to the fretboard, and you can play more comfortably. When you stand up, you have to worry about how high/low you have the guitar because that will not only change your angle of picking, but it will also affect your fretting wrist and finger reach.

For me, the biggest change is getting used to my picking hand. If feels wierd because it is at a completely different angle/position than when sitting.