olyloh6696,
I haven't actually tried putting another case on top of my Desire, so I can't tell you. But don't worry, I found the same thing, the screen protector has this abnormal long white scratch on it (quiet visible, along with numerous others which can be seen at obscure times), which only came about after using an alcoholic wipe on it, so I don't know whether it was my own fault or what.
I currently only have the front screen protector and the back protector on, unfortunately after about 3 months of use (and possible incorrect application) the sides started peeling at the top, which I then removed them. I am pleased knowing that the back is protected at all times, it is a good "body" protector, but not a screen (due to scratches and glare).
I will admit though, I am tempted to order the invisible shield for the Desire S, but I want a little more protection this time around particularly on the sides of the device, which I'm hoping the Case-Mate barely there will at least provide me (ordered it last night).
There is another company which offers a protector similar to the invisible shield, seen it on either this forum or the HTC Desire part of the forums, had a quick look but I can't seem to find the thread, but that company offered matte versions and even coloured versions which looked very appealing.
Toje2,
That case looks as though it could survive a nuclear fallout haha.