If you're fxp from one site to your own, then you can put those 100% complete files on you flash fxp's filter list (if you're using ffxp that is)
You can also disable creation of folders or uploading of files with those names in ioftpd.ini or with zr-tools as Harm mentioned. To do it in ioftpd.ini add the following under the VFS section:
Code:
Upload = "*/100% Complete*" !*
MakeDir = "*/100% Complete*" !*
PS. I haven't tested exactly those lines above, but I do know that it works if the tags doesn't include any space. I added quotes around the path so it probably works, but I'm too lazy to test it myself :P