Hi Aidan,
Sounds like your Polar Alignment is off.
Go to the brain symbol and turn off the guide output, turn on the cross hairs and capture images again, select a star, put it in the centre of the cross hairs and watch it for about 1-2 minutes. As PHD is NOT telling the scope to move (because you disabled the output in the brain) you should see if the star moves away from the cross hairs.
What I do to align the scope using the guidescope and PHD is just this, but first I select a star either east or west about 30-40 degrees up from the horizon. If the star moves off the cross hairs, adjust the ALTITUDE bolts (the up-downs) and see if you can slow down the star's drift. Recenter the star after the bolt adjust. After a while if you get some improvement, slew to a star overhead (so the scope counter weights are horizontal and the tube is perpendicular to the counterweights (like a T) and pointing pretty much straight up. Repeat the drift check with a star in the cross hairs and ONLY ADJUST THE Azimuth bolts (the left-right ones) until you can slow down or STOP the star drift.
Go back to an east or west star, check it again, adjust as necessary, rinse and repeat and see if you can keep the star IN the crosshairs for a few minutes and then turn ON the brain guiding output. CHECK the box that tells the program to FORCE the calibration, wait for the calibration to finish and then see what the graph does now.
That's what I do, once you think you have it dialled in, MARK the tripod leg positions on the ground so you can plonk down the scope next time and get going quickly again.
Of course I would also check the tube is balanced in RA and DEC as well as if it is too heavy, PHD has a bugger of a time pushing and pulling the scope if it is heavy one side or both....
Give this a go, sorry for the essay
Cheers
Chris