crazygazza, you could use VirtualDub to pre-process your videos before converting to .amv format. There is a sticky thread guide by tadad1 on using VirtualDub
HERE
There is a filter function within VirtualDub that rotates the video to 90degrees.
Just add the Rotate filter by clicking
Video >> Filters >> Add >> Rotate click OK, and select either 90degrees left or right. Then process the whole video.
Hope this helps.