Hi Dunk,
Sorry to hear that you're having drift woes! I'm not familiar with your specific setup or workflow, so I can only really tell you what has worked for me.
My EQ6 came with SynScan hand controller firmware 3.33, so I can't comment on any versions prior to that. If you've had drift-free sessions in the past, I would suggest updating/downgrading the hand controller and/or motor controller firmware only as a last resort. Personally, I feel inclined to go back to 3.33 since I find the new two-stage polar alignment procedure to be no more accurate than it was in 3.33 and if anything, more cumbersome.
As Astro_Bot pointed out, I agree that it's probably a polar alignment problem more than anything else. I'm very picky about polar alignment accuracy and not being able to resolve Octans from my location, I rely on the polar alignment routine in the hand controller.
What I've found works
really well if you want a very accurate polar alignment, is to do both the 3-point mount alignment and polar alignment routines using a guiding camera with a high-speed readout (a modified webcam will do, though) and a barlow lens -- the higher power the better.
I use PHD 2 to see what's happening in the camera and, after enabling the on-screen crosshairs and adjusting the focus so that the star is bloated enough to fill the centre circle, bring it into the middle (see example image attached).
Once you've done both the 3-point and polar alignments using this method, you've got an excellent starting point for making adjustments to compensate for any drift as it's much easier to see the drift on-screen than it is through something like a 9mm illuminated reticle eyepiece.
I've been able to achieve =< .175" accuracy using this method.
If you want PHD 2 to show you how much error you have in your PA, you'll need to arrange an autoguiding setup first using a small refractor or an OAG. Then, in PHD, just turn off Dec guiding and it'll give you a readout on your PA error.
I suggest powering off the mount after doing the polar alignment and then going through both the 3-point and polar alignment routines again to confirm and refine. It can take a little while, but if you don't have a permanent setup and want the accuracy level, it's worth it.
Be mindful of the fact that if the mount is not sufficiently balanced (or if it's overloaded), it will impact the accuracy of your 3-point alignment, which in turn will impact the accuracy of the polar alignment routine in the hand controller.
Disabling the auxiliary encoder via the appropriate menu in the hand controller will improve pointing accuracy too, so you may like to give that a go if you've not done so already.
Good luck!
Cheers,
Brett