I'm sure you've had someone mention this, but.. I think the config.txt file is read as one of the very first first tasks so perhaps Berryboot has moved it and/or is reading a different copy of the file? i.e. one that does not have the rotate=3 (or whatever you rotate the display to) command in it.
It took me a long time to get my display booting and running in portrait mode, and I feel your pain. My problems were with faulty memory card supplied with the Pi. (USA distributor)
Once I've got this thing configured the way I want it (which is a very steep learning curve for me..) then it makes sense to do a capture of the memory card so I have a back up. But damned if I can find a program that will let me do that (in windows; because I can't put two memory cards into the Pi) so off I go to look yet again.