Matt -
I have seen this, and it is frustrating.
From what I gather, the Publishing Wizard keeps track of the
files published, along with a checksum and date for each file.
Subsequent uploads will compare all of the files, and then only
upload those files that have changed. The more files, the longer
the list it becomes, and the longer it takes to check each file.
This makes for a very slow publishing process the first
time, but subsequent updates should move more quickly.
You do have other publishing options, ftp'ing, or using the
FrontPage upload - but these are transfer protocols designed for
uploading to a web server. Since you are on a network, you could
just copy the output to the network drive.