I have the same problem.
I'm using: USB loder 1.1, (starting up as a channel)
I have a: PAL Wii, Windows Vista Ultimate 32 bit (running in administrator mode)
Disk is an: Samsung Laptop sized disk with a sharkoon case around it that uses power over USB.
Disk setup: 120 GB partitioned in 2 partitions one labeled H and the other is for Wii games, size 20 GB.
Here's what I found out so far.
If I format the drive trough the Wii it works without problems. I can dump my games on it and they run without problems. If I then want to use the drive on my PC it can't find the patition and says it's accoladeed space (none partition) So formating trough the Wii makes it unusable for PC in any program.
Then I reformat the partition to Fat32, Label it with: N an let it init with your program. Dumping iso's works like it should, no problems so far. If I connect it to the Wii USB loader says that there are no usable partitions an want to create one.
Any thoughs about this problem?