heh, yes i prefer linux too for formatting. Mainly coz it "works"
A good win32 based solution is Partition Magic 8. Ive used that many times to great success.. BUT that is not free.
Windows based systems see removable cards as just that, removable, NOT fixed. You can screw around with fdisk / format / diskpart in a cmd prompt.. or you can do some reg hackin.. not TOO hard.. Ive personally never tried it, BUT it seems reasonable enough.. (i dual boot arch / winxp)http://www.1src.com/forums/showthread.php?t=133718
From my quick searching around, there is no available (free) software for doing this task. I know from experience that part magic8 reboots at some point to "finish the task". I suspect this is because windows wont see th disk properly.
And just spoke to a mate, he will start workin on a solution now.. he is a fairly hardcore programmer, ill post some results about it later. Will be a win32 based prog, fairly "simple".