I fitted my Artic Cooler a couple of months ago, and it has been working fine,
however I too noticed when I fitted it that the original heatsink was slightly
raised so it made better contact with the core.
I left the shim which appears to be epoxied in position on 4 sides of the gpu
and AIS I've had no problems, even with a decent OC, however I've noticed a few
postings in here which advise that the shim should be removed, anyway I couldn't
rest until I took it off again to check it out!
On carefully checking the height of the shim with the core using a engineers
slip gauge as a straight edge I found that the shim is exactly the same height
as the core... in fact using the thinnest paper I could find... I couldn't
remove the paper from under the core without tearing it when I pressed down with
the straight edge.
In my case I decided to leave the shim in place again, as there seemed little
point removing it... plus AIS it appears to be epoxied into position, this was
on a PowerColor 9800 Pro card. FYI the core did appear to have been making good
contact with the Artic Cooler when I lifted it off to check.
Obviously it all depends on the height of the shim, but if one puts a straight
edge across to ensure its not higher than the core then it can be left in place.
At least I wont keep wondering now!

))
Regards
Mike