This is probably down to your anti virus.
You can test this by temporarily disabling it, loading FlashFXP and scrolling through the file list.
A basic kind of explanation for this behaviour would be as follows:
You scroll through your files in FlashFXP, it has to display the icons for those files.
Those icons are usually stored in an EXE or DLL file, which much be accessed in order to display the icon.
Any decent AV program scans on-access, so for each icon that gets displayed, it's possible that your AV had to scan the file that was being displayed or at least one other file to display the files icon.
Of course, this scanning will slow down your file listing.
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