The first part I don't quite understand what you mean, but the second part, as far as I know, if you took the pictures sideways, they don't auto-rotate on a computer, easy to fix though, you just right click and choose Rotate CW, or CCW
Ur right it is a little confusing. I did a drag and drop using explorer (WINXP) to the photo folder on the phone. They were dropped in the folder on the iPhone called Photo Libary. Then when I took some pictures and they did not go in the same folder but a new one created by iPhone called Camera Roll. The newly taken pictures when transfered to the computer laod 90° CCW.
I hope this description is better. I realize I can rotate them, but it sucks to have to take yet another step because of poor software engineering.