What if you created the partition for your PS2 stuff first, before you create the 2nd partition for your Wii stuff? It should be an adequate workaround until the fix yoshi314 mentioned is implemented.
Marking the Wii partition as "hidden" might not help, depending on the implementation of the filesystem driver part of the USBHDFSD driver.
Unmodified SCPH-77006 with SM 3.6
SCPH-39006 with M-chip modchip, SCPH-10281 NA and refurb Seagate 80GB HDD
SCPH-10000 v1.00 with SCPH-10190 PCMCIA NA and SCPH-20400 HDD unit