Thanks Hibern. I have put in about 3 hours of rigid testing, and can now produce desired bugs at will. I have boiled it down to the wiiflow.ini file, and how it handles loading covers using the "data_on_usb=no" command. On my drive where a FAT32 partition exists, I place a wiiflow.ini that I created with notepad, with the data_on_usb=no command. The covers download to my SD fine, and show in the loader with no problem. Wii Sports Resort (problematic game/002 fix) launches fine, as do the other 17 games on this drive. Then I power off my Wii.
From here, I plug in my fully partitioned drive containing 236 games, and try to launch Wii Sports Resort (which just worked on my 2 partition drive), but it freezes at black screen, wiimote disconnects, and I have to hard-reset the Wii. Now that I've had this failure, I power down my Wii completely.
Then I plug in the first drive that worked (2 partitions) and Wii Sports Resort (which just worked on this drive) now won't load. I can only guess that something is being written to the wiiflow.ini when I plug in the other drive, and then causes some error to be written to my settings, which is why the drive worked just moments ago, now won't load any of the 18 games on it.
For the heck of it, I deleted my wiiflow.ini altogether, and decided I would only use my fully partitioned WBFS drive with covers on my SD. Since there is no FAT32 partition on it, I don't need to manually edit the wiiflow.ini, and can let the loader create it naturally. Wii Sports Resort loads fine, but when I reset/shut down, and try to load a second game, but no games will load from here on out. I'm using cIOS_rev14 on a 4.1U Wii, so this isn't an error with my softmodding, as other loaders don't produce these results. I hope this info was helpful in resolving this issue, and I've read a couple others with the same problem, so I do believe it's not my error. Feel free to contact me if you need any more input or testing.