Are you using firefox? I have seen some problems with firefox where it doesnt like file names with spaces in them. Here is the file name it saves as when using IE6:

Repository Users Guide[1].3.01.09.zip

Notice that it cuts off everything after the first space. I am not sure why this happens, but it also happens for me too with FF 1.5.0.2 Both the documents module and the repository have this problem.

I have no idea what the fix is for it or what causes it, but i end up going into the db and replace spaces with underscores in the filenames, and then change it on the server.

I'm not sure, but i did some searching on the cause.

Seems that in the code where the file is pushed to the clients browser, the filename should be enclosed in quotes for firefox to get the full filename with extension.