I have the same problem with VS2010 and .js files and FTP publishing, except that I am using VSS.
Sometimes some files are not published after minor changes.
What I am doing is removing them from the server before publishing. I tried adding or removing a new line at the end of each file and it seems to work much faster than deleting files.
With two previous solutions or workarounds, the file may be skipped.
Another (not very effective time, but possibly better) solution is to select the publication option "Delete all existing files before publishing", but this significantly increases the publication time from several minutes to more than thirty minutes.
Also, I have this problem when I am the only one working on a project.
I know this is not an answer, but my first post is here, and I'm not sure how to reply to the message.
EDIT: My workaround (hopefully the best solution is found) is to delete all .js files on the server. This slightly increases the publishing time, but not as much as using the "Delete all existing files before publishing" option.
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