I haven't got the same mount, Steve, so I can't comment on the intricacies of the EQ6.
It sounds like the polar alignment is well off for the star to disappear as quickly as you describe, so some
basics to check...
1. make sure your mount is tracking (at sidereal rate).
2. Check the +24 degree magnetic offset is correct and you've made the adjustment the right way on the compass.
3. Check your time on the mount. My CG5 obviously didn't keep time while I was doing a 3 star align, so depending on how long it took (sometimes 30 minutes or more if the stars were unacceptable and I had to choose new ones). This meant that the mount was out by the same amount in RA (until I bought a GPS unit

).
The procedure I use with my mount is as follows (it isn't the same mount, I know, but I just offer it for food for thought):
1. I do a rough alignment by compass, balance it all and set up at home position and switch on.
2. I select a Quick align. On my scope this does not actually align on any stars - it just models the sky at that time (remember I now have GPS so the mount time is always accurate).
3. Drift align.
4. If I was accurate goto, I the power down the mount and on restart I do a three star align.
Food for thought.
Al.