I haven't had this specific issue but when I was originally softmodding my Wii, the process took well over a day, went at a ridiculously slow snail's pace. This was before anyone knew that leaving in GameCube memory cards affected the process. That said, you may find luck ensuring ALL peripherals/cards/controllers are removed from your Wii and reinstalling/updating your ios/cios's. I know you asked quite a while ago; I would've likely lost hope but its worth a shot.
For shits & giggles you might try leaving the GC controller unplugged until you load the game using the Wiimote, then plug in. In your case it may seem getting the Region correct is the most reliable fix.
However, I did find a problem using the plugin modded off of snes9xgx_4.3.4: snes9xgx-mod11.dol. Just like you, loading SNES9x GX via the homebrew channel and using its built-in interface to load ROMs worked great. Using the plugin would crash every single ROM except those in zip containers. Most of mine are in 7z files, and even the ones with just a single ROM inside would still crash, forcing a hard reset (power off & reset buttons were unresponsive, you'd have to hold the power button to turn it off and back on again).
The solution was repackaging them in zip files. I noticed the few I had in zip files to begin with were the only ones actually functional when loading from within Wiiflow. No issue loading from within SNES9X GX's interface. I'm guessing the extra overhead of uncompressing a 7z file became too much with what Wiiflow already has in memory, or hasn't yet freed enough of itself from memory during the loading process. To be honest, I haven't yet updated my cios/ios's in a couple years either, so that may play a part too, but there is definitely something else at play using the plugins and the way they hand off control to the program that affect SNES9X GX in some way. The best way to have this fixed for good is getting one of the Wiiflow devs to look into it, but our seemingly isolated cases may not be pressing enough to warrant the time to find the bug(s).
If you too have had my problem, I found two things helpful:
1) Knowing more about ROM notation:
https://64bitorless.wordpress.com/rom-suffix-explanations/
2) And a handy tool that repackages ROMs into either ZIP or JMA container files called UnGoodMerge:
http://www.users.on.net/~swcheetah/sam/UnGoodMerge.html
A discussion on the tool I found here:
https://sourceforge.net/p/goodmerge/discussion/418284/thread/88e12ac0/