Good to hear you've nailed the possible problem Paul.
I went through a similar scenario a week back trying to sort out the elongated stars in my images, and by process of elimination found the side by side bar was causing real bad flexure which was identified by slight diagonal star trailing in my images.
I changed it to a piggyback setup and that trailing was eliminated, except I now had trailing running vertical. Changing PHD settings made little difference and this ended up being an RA counterweight issue.
Thats now solved with additional weight, now I believe I have focuser tilt issue to deal with, which is identified by elongated stars in bottom-left and top-right corners but not at center or the other corners.
With breezes about each session I always thought it was PHD and the gusts of wind causing the problem.
Thanks for sharing your troubleshooting results. Once I've got my scope sorted I'll most likely also post up my troubleshooting results as originally most people mentioned that my images could have been the result of a pinched-mirror
A couple of guys have mentioned to rotate the camera at 10degree intervals during your imaging session, and watch for the changes that may highlight a focuser tilt/weight issue or sag problem.