Might be a daft question but is the cover located properly into the lower plastic part of the cover?
From memory there are like two tabs that slide down behind a lower cover assembly which help hold the upper part in the correct location.

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Goldie the track car.

Yeah it can be removed and refitted in situ. It's a bit fiddly getting to some of the bolts that secure it but it is do-able.

I've just been searching for any pictures i might have to try and show you what i'm on about.
In the image below one of the bit's i'm on about would be at around 2:30 if the crank pulley was a clock.
IMG_0886 by Steve Count, on Flickr

In this one the other side is visible at around 8:30
IMG_5140 by Steve Count, on Flickr

The top part of the cambelt cover should slide down and slot behind the bottom plastic part of the cover which is secured with the two capscrews shown in the images above.
If the cover isn't seated correctly then i reckon it would be out far enough to rub on the aux belt.

To remove the top part of the cambelt cover theres the three captive (i think from memory) bolts around the top edge, then i think two nuts down the centreline on the later models, on the earlier models i think theres a metal strip that you may need to slide up or down to release the cover.

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Goldie the track car.