usually, the issue is caused by "returning to" an old version when exiting nintendont.
reloading an old version (the full channel) which doesn't have the new settings cause these settings to be deleted from the GXglobal.cfg
If it returned to the correct revision, your settings would still be there as they would be known and not deleted.
did you try to do it manually ?
1. run USBGX from HBC.
2. set a setting you can easily check later to see if it's preserved or lost.
3. exit USBGX (not from launching nintendont, just exit > to HBC or system menu)
4. from system menu, launch USBGX channel (forwarder)
5. check your setting, is it good or lost ?
if it works, and your setting is preserved, then it's related to nintendont only ?
run USBGX -> nintendont -> exit back to return to USBGX.
setting lost?
I could ask if the lost setting is only set during the "last session" before launching nintendont, or if even very old changed and already saved settings in multiple previous sessions were lost too?
If it's affecting only settings set in "last session" then there's a setting saving bug when launching nintendont. can be fixed easily by forcing a setting save before launching a game.
if it's affecting old changes, then to me it looks like a conflict of different version, and I don't know the cause if you really have the same version.