I found that out as well when I tried to quieten a Shuttle SV-25. The acoustic mat reduced the noise a little but it got very hot inside due to the insulation effects of the foam. Also it really smelt and even after a few months it still had a lingering plastic/petroleum odour to it.
It's quite difficult to get the stuff off as well I found!

In the end I replaced the CPU heatsink/fan, PSU fan and casing fans and it's much better now. I wouldn't want it in my bedroom but it's okay under my desk.