I noticed that when I open "My Documents", I see transparent icons that start with the "~" or "~$" symbols. Is that normal?
That sounds like temporary files that are hidden, they should not show once you have run OTL cleanup. If they still show then
- Open Windows Explorer by right-clicking the Start button and left clicking Explore
- Then select the Tools menu and click Folder Options
- Select the View Tab, Under the Hidden files and folders heading select Do not show hidden files and folders
- Check the Hide protected operating system files (recommended) option
- Click OK
I have an external hard drive on which I backed up all my files. Should I have scanned that hard drive with any of the tools you suggested in this thread?
A full scan with your antivirus should be sufficient.
When I ran WinPatrol, it said "A change had been detected in the following Registry Location which you've asked to be monitored. Is changing this value OK? Software]Microsoft\Internet Explorer\Download CheckExeSignatures:no" Should I click "Yes" or "No" for that?