First thing to remember is that not all USB Loaders will be able to read NTFS formatted partitions with all cIOS. What version of USB Loader GX are you using with what cIOS?. For the latest USB Loader GX, I recommend using Hermes cIOS v4 for NTFS as its old and proven. Also be careful about what type of partitions you have setup. All partitions must be primary partitions, logical partitions will not work, and your WBFS primary partition should be set to active.
That said...since you have decided to use a NTFS formatted partition, why not get rid of your WBFS formatted partition and just set up a WBFS folder with WBFS files of all your games on your NTFS partition? This way you simplify your setup and have more freedom to use space as you see fit without any predetermined partition sizes to worry about later...
-[]D