with my mSR i have 4 batteies in rotation, and notice that when i switch them my rudder trim goes way out of wack so much so that one battery i need to trim all the way left. and the other all the way right, and then sometimes thats not even enough. and the other two batteries run properly! is there somthing im missing here?? or when i switch from battery to battery should i be shutting the Tx off? sorry for the noob questions im just trying to figure this out.

Mark the batteries with a magic marker, 1, 2, 3 & 4. Make note of each battery and see if the same battery give you the same problems. It may be a battery issue.
Also, try turning the TX off, also. However, I don't think that should make a difference.

they should run all the same, except for the run time. if your putting them in all the same, then why would your trim settings change?

Perhaps you are moving the heli as you put the battery in. Make sure the heli is on a flat surface as soon as possible after you connect the battery until the gyro initializes.

really i did not know about that thanks for help, i will try tommorow.