What version of VP are you running?
In 4.10 here, three image clips of varying aspect ratio were rotated after being placed on the timeline, using the right-click|ROTATE option on each in the image BIN.
Next two video clips - - one a 16:9 Mp4 and the other a 4:3 wmv file - were handled in the same manner, using the right-click|ROTATE option on each in the video bin.
In all instances, the rotation was shown in both the bins and on the timeline and it "stuck" after the two projects were saved to .vpj files and later restored.