Dios Mios Issues

I have been using Dios Mios (Not Lite) in conjunction with CFG USB Loader to load Gamecube games from a 16 GB PNY Flash Drive. Things work fine when loading the games from there, but when playing most retail discs, the game freezes. This usually happens when loading a file or menu: for example, I can boot up Metroid Prime 2 just fine, but the game crashes when loading my save file. Do you guys have any ideas as to why this is happening, and how I may fix it? I have looked all over the internet for answers, but have found none.
Thank you,
BLsquared.

UPDATE:
To those who also have this issue, do the following:
-Install a clean MIOSv10 over DIOS MIOS.
-Install Nintendont (a GCN interpreter for Wii, vWii and WiiU that doesn't need the MIOS)
-Edit the meta.xml for CFG USB Loader to enable AHBProt. See the Nintendont OP for details.

Now you should be able to run retail discs fine, while still being able to play backups through Nintendont. Thanks to Cyan for helping me out!

 

Thing is, it worked before installing Dios Mios, and Metroid Prime 2 is not the only game that suddenly doesn't work; in fact, only two of my retail Gamecube discs actually run, and they're much more scratched up than any of my others.
I did try ripping MP2 as a workaround, but it kept failing, apparently due to "unclean disc". Will try again after a good cleaning.\
But, when the real disc crashes during loading my game (or starting a new one), there is no "Clean Disc" message or anything as that; usually it would have one, right? Assuming cleanliness is suddenly the issue with all but two of my games...

 

But Dios Mios Lite works only on SD cards; I have no SD cards larger than 2GB. Also, I found this thread while Googling: https://gbatemp.net/threads/dios-mios-works-with-retail-discs-or-not.338030/
Sounds as my using CFG may be the problem; this guy suggusts using USB GX. I'll try that....
On a side note, I tested my 4 Gamecube discs and found that 2/4 of them work:
Don't Work:
Disney's Extreme Skate Adventure
Metroid Prime 2 Echoes
Work:
Lego Star Wars II
Frogger: The Rescue

Don't get why MP2 and Skate don't run; and they both stop when loading a saved file. Hmmm.... Still going to test out GX.

 

Thanks; I cannot get GX to work (Freezes at "init USB Device"), and I was using DM 2.8 awhile back and it failed to work with GX. Back to CFG it is.
The drive is a 16GB PNY USB 2.0 Flash Drive. I think it's on the list of working things; plus, this is the only place I have issues with it.
I'll look at other DM versions and see what I can come up with...

 

OK, will try; I'll also install DM 2.10, see if that changes anything.

EDIT:
OK, tried changing IOS to 58; says I have no IOS58 and changes it to 200. Guess I don't have 58 installed...?

 

OK. I'll go with 2.11 then; assuming I don't already have it...

EDIT:
Already have 2.11 installed. What now? Guess I'll install ios58 for good measure. Looks like its for USB; maybe that's my issue?
Re-EDIT:
Already have IOS58. ugh....

 

OK: back to square 1. Time for a recap:
Dios Mios 2.11- installed
IOS58 - installed?
USB Loader GX - Does not work; says I don't have IOS58, but IOS58 Installer fails (But the corner of the screen says I'm running IOS58 already)
CFG Loader - Works fine
YAWMM - Fails to install anything: error after selecting WAD. Thus I cannot install old Dios Mios versions.
Metroid Prime 2 Disc - Still doesn't work, and cannot be ripped (Will give Disc Dirty error or altogether freeze and corrupt my flash drive)
Might try running someone else's backup of MP2 and see if it works; if it does, than it must be an issue with my disc. If it doesn't, than it's a DM compatibiliy issue.
Any other ideas?

 

Nope; never used pimpmywii. Should I?
Anyways, I'll pass on USB GX since CFG seems to be working as normal. Still have yet to test the backup of MP2; Thanksgiving and all.
I'll look more into the YAWMM thing too.
Thanks for all your help thus far.

EDIT:
I saw an alternate loader called nintendont; do you think that maybe I could use it as an alternative to Dios Mios, or should I not since, it being an interpreter, it may not have the compatibility and speed of Dios Mios?

 

OK. Looked into Nintendont:
It does not support retail discs.
So, here's the new plan:
Re-install old Mios.
Install Nintendont for backup loading.

Theoretically, this should fix everything!

EDIT:
Yup, that fixed it! I ended up using MMM to install the old clean MIOSv10 wad, (turns out I was loading the wrong IOS!) and installed Nintendon't and set up CFG USB Loader to use it instead. I can not only run the MP2 retail disc properly now, but I can even run it's backup from Nintendon't just fine!
Yay! I'll update the OP to better inform others with this issue.

Thank you so very much for your help, Cyan!