The only difference I noticed whan adding a FAT32 partition (not NTFS) was that windows became much better at detecting the drive. I noticed no difference with WBFS manager and my GX loader.
Setting partitions as primary and active is done through disk management in Windows.
Just for testing why not try Waninkoko's SD/USB Loader v1.5, it's a basic program but gives error codes when stuff doesn't work, maybe it will help. I always find the GX and a few others either work or not, but give no clues when they don't.