A version of WBFS Manager is 3.0. Don't now if it is important but I created those wbfs files with x32 version. My Windows version is x64 but WBFS Manager x64 crashed several times.
Here are the directory list on my USB flash. Other apps including Homebrew are on the SD card. All wbfs files have proper names (id_numer.wbfs).
Volume in drive J has no label.
Volume Serial Number is 2C05-6AF0
Directory of j:\wbfs
08/24/2012 02:06 AM <DIR> .
08/24/2012 02:06 AM <DIR> ..
08/22/2012 12:17 AM <DIR> ABBA - You Can Dance [S2EE41]
08/24/2012 02:06 AM 0 Directory_Listing.txt
08/20/2012 09:09 PM 141 FileDirCheck.bat
08/19/2012 11:46 PM <DIR> Mario Party 9 [SSQP01]
08/19/2012 11:23 PM <DIR> MARIO SPORTS MIX [RMKP01]
08/19/2012 11:20 PM <DIR> NBA JAM [SNJP69]
08/19/2012 12:11 AM <DIR> Pro Evolution Soccer 2012 [S2PPA4]
08/19/2012 11:20 PM <DIR> Wii Party [SUPP01]
2 File(s) 141 bytes
8 Dir(s) 2,840,125,440 bytes free