Yep, theres is a difference unless you strap the guitar up to your chest. I use to practice only standing since it was such a pain to learn something sitting down, then slow it down a bit to be able to play it standing up. The best way I fixed that was by setting the guitar on my left leg, and have the "ass end" of the guitar pushed up against on the other, with the strap button keeping it from sliding down. It makes things easier to play sitting down and I never have a problem switching from sitting to standing.

Its funny because I didn't start doing that for that reason. I saw a video lesson by Mark Tremonti and thats how he was sitting with it. I though that was the proper way to sit with it, since the only other video lesson I saw at the time was Esteban's and that was with an acoustic.