Errr, it seems that you (or some program you've used) has unZIPped the .ZIP files in \ROMS (and probably other) directories.
You don't want to do that

You're going to have to clean out all the files that have been unpacked...you just want the original .ZIPs in the various ROM/sample/etc directories.
As for an explanation of that error, it's because you're hitting the maximum-number-of-files-in-a-directory limit in the filesystem...you're also needlessly transferring thousands of files and many gigabytes more than you have to because you've unpacked the .ZIPs.
Yeh, looks like your newsreader has extracted all the zipped files after download..
SABnzbd and some other readers do that by default.. Just turn it off, or make it say something like "repair only"
Haha, now I see it! You were right! SABnzbd unzipped everything. Re-downloaded it with just 'repair' as parameter and it FTPed without problems!