Windows Me ScanDisk Problems

Hello,

I have recently been plagued with spyware and adware problems and followed the instructions on the virus forum.  My computer was working well after that.  However, when I tried to download new software I upgraded my internet explorer in order to support it.  Unfortunately, after this I am experiencing even more problems now.  Any time I shut down my computer correctly and turn it on again, my ScanDisk runs and says it was due to improper shut down.  However, it goes on for hours and then tells me that it started about ten times and couldn't run because something was writing on the disk.  Is this because of all the spyware/adware/HJT stuff I download before?  Please help, I am not sure how to solve this problem.  Thanks!