I've just replaced my window seals, which is a bastard of a job at best, but the
new seals appear to have this issue where once the window is closed, it can still be pushed in another 10mm or so.
The locking gizmo also catches on the bottom of the rubber.

Any of these problems common to aftermarket seals?

I think i had some small issues with the bottom of the frame catching the rubber. I solved it by not opening the quarter glass's anymore. I also fitted my rear view mirrors outside the quarter glass which prevents me from opening them anyways....

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http://www.youtube.com/user/Hanras

Yep there a problem alright...Have your door open as well as quarter window,and carefully with a small screwdiver push the rubber under the quater window as your shutting it...Work your way along...And as said before leave the window shut...if you open it the rubber will pop out again...they can be a pain!! cheers..

Not really. This is a not an uncommon problem which sometimes occurred with original rubbers.

Really effing annoying. I cured it once by swapping the 1/4 vent glass. What I discovered was the bottom of the framed had 'spread' or dropped away from the glass probably from normal wear & tear.

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1967 Cooper S - new front bearings to do.
1965 Cooper S shell - Slow progress. No time or money!
1966 Deluxe- next rustoration!
Mk 2 & XJ6 Jags. Less said the better.