Well, there are some rare occasions where applications place files in particular clusters as some sort of "copy protection." I personally hate this technique, but maybe some of your apps are affected by this. [Internet Explorer] does not have this mechanism, so maybe the defragger did not handle open files correctly, which corrupted them. I cannot tell you much about this defragger, but you should check your disk for possible faults. If there are no hardware defects, I guess it will be related to corrupt files. If you want to check, reinstall the apps and re-run the defragger. If the problems recur, it is some problem with the defragger. Maybe you [should] check out some other defraggers, which are available on the Web.
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