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Have you rebooted with the CD still in? That's the only thing I can think of. Never installed BackTrack, but with other live/install distros the install icon disappears once they're installed.
If you have installed Backtrack to a different partition it can't make Windows work slower, only one OS at a time is running in that case, not both at the same time. If you have installed it into a VM the it will of course make your Windows slower, like any other resource heavy program.
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