NamikazeBurst 
Your not running out of space or anything??
I could upload the WBFS file directly to make sure it's not just a transfer issue, i.e. just copy using windows, so you can skip the use of Wii Backup Manager.
P.S. I actually run Wii Backup Manager directly from my Wii HDD (while hooked to my PC obviously) I use a rather larger 2 TB drive though with 3 Partitions on it 1 for a mix off GC and Wii, 1 that is full of Wii games and a small one for homebrew
There is a limit to how many Wii games you can have per partition though, think it was around the 500 mark though, that is one of the reasons I have a few partitions, I am sure that is just for retail Wii games though so Wads GC Homebrew and other software types are not counted in that
:/ A reformat might be in order, but before that do a scan on the drive with windows, right click on the drive, hit Properties and click on the tools tab, use the Error-Checking & Defragmentation tools
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