@Alexander the -force option doesn't change the results
@Mathieu removing *.* causes the whole command to return nothing. Additionally, I've run this command as an admin and not as an admin under my own account and under a network admin account with no difference in result. I know my account can at least access all the folders (certainly more than just the root and one random subfolder) and the network admin account can access anything on the network. That being said, issue #2 is a non-issue now since I found out some network files will have a creation date newer than their modified date if they've been copied from another location.
@Mike I can certainly try to install PowerShell on my 2003 server, but it will be a major inconvenience if that requires a restart. Additionally, do you think running it locally will return more results? My problem right now isn't that it takes a long time to run the command, it's that it only returns results for the root of the folder and one folder out of at least 100.