Currently WubiBCD executes BCDedit commands without waiting for the previous ones to finish. It turns out that bcdedit.exe (which WubiBCD uses to modify the BCD registry) does not support multi-threading, and will not properly deal with more than one request for modification to the BCD at the same time.
For instance, an entry is created, but while its drive is being assigned WubiBCD also attempts to assign it a path - one of the two properties (path or device) is not properly saved, and therefore the entry either won't appear in the list or will appear but won't work.
Fixes (just some samples):
http://ubuntuforums.org/showthread.php?t=778772
http://ubuntuforums.org/showthread.php?t=781941
Basically anywhere where one of the Wubi entry's properties are missing in the BCD debug output.
