Mick,
I am unable to reproduce this issue. I just moved my Favorites pane to a different location (between the Navigator and the Tasks panes) and sized it the way I wanted each of them to be, quit PM5, and relaunched it. When PM5 finished launching the panes were in the correct order and were the correct size.
Now, my build is newer than the one you have and I have made some changes to the Workspace persistence so maybe that's why I can't reproduce the problem.
Please evaluate the next build which should be coming soon.
Thanks,
-Kirk