After-market glass window top not fitting?

[soggyinmilk]

Happy New Year y'all!

I have an 02 Boxster that we just replaced the top on. The old vinyl window was shot and we decided it was a good move from the feedback on this forum and a few shops we talked to.

It was supposed to fit fine, but now that it is in there the top doesn't fold down completely. Once the range is cleared and it engages the sensors, the pop-up cover is sitting about a half inch or so above the rear fenders that it has always been flush with.

Has this happened to anyone before? The shop I chose in Huntington Beach is telling me that now they have to remove some of the engine cover foam to make it fit and I'm saying WHOA! I don't want them screwing anything up. Is this just a bad top? They assured me it was a GAHH A5 but didn't buy it from them directly, apparently.

Let me know if these guys are taking me for a ride.