more info please!

what version of wiiflow are you using?
is it Abdallaterro's masterpiece mod version?

just so you know official wiiflow's were never updated to work with the latest nintendont. you have to use Abz's masterpiece mod or wiiflow lite. try Abz's first.

 

wiiflow has no idea what settings you have used when loading nintendont from hbc.
however all the settings (per game) are saved when you launch games using wiiflow.
So all you need to do is set the options in wiiflow (only once) and have the game launch with preferred settings thereafter.

P.S> After launching GC games via wiiflow, you have the option to cancel autoboot using "B" button
So when you cancel the autoboot you can go to nintendont settings and make sure all the options are the way they should be
For MC emulation you have 3 options and they all should work fine (none single and multi)

In case you want to make global Nintendont options for all games continue reading the spoiler:

Warning: Spoilers inside!

WiiFlow and Nintendont default options:
* Nintendont is default loader now
* GC mode always enabled
* MC Emu on by default using 2mb files
* Pressing B for Source Menu is enabled by defaut too

These options are now global settings in /apps/wiiflow/wiiflow.ini so change the default value to your liking
to enable use "yes", to disable use "no"
-------------------
For 1076 mastermod:
-------------------
USB_HID=yes (for Disabling HDD Pinging under [dml] section)
NATIVE_CTL=yes (for native GC controller under [DML] section)
Deflicker=yes (for force deflicker video under [DML] section)
screenshot =yes (for wiiu widescreen under [DML] section)
dm_widescreen=yes (for widescreen patch under [DML] section)
For MC Emulation: (under [DML] section)
dml_nmm=0 for disabled / dml_nmm=1 for enabled / dml_nmm=2 for Multisave
enabled is the default using 2mb files - multi uses 8mb files (one for us/pal one for jap)
For launching Wiiware/VC using Neek2o:
useneek=yes (under [NAND] section)
For using Wii games private server:
private_server=yes (under [Games] section)
-------------------
For 1054 mastermod:
-------------------
USB_HID=yes (for USB Controller under [dml] section)
NATIVE_CONTROL=yes (for native GC controller under [DML] section)
WIIU_WIDE=yes (for wiiu widescreen under [DML] section)
dm_widescreen=yes (for widescreen patch under [DML] section)
For MC Emulation: (under [DML] section)
dml_nmm=0 for disabled / dml_nmm=1 for enabled / dml_nmm=2 for Multisave
enabled is the default using 2mb files - multi uses 8mb files (one for us/pal one for jap)
For launching Wiiware/VC using Neek2o:
useneek=yes (under [NAND] section)
-----------------------------------------------------------------------------------
P.S. delete \wiiflow\settings\gameconfig2.ini file to restore default configuration
-----------------------------------------------------------------------------------

 

This thread hasn't had a reply in 4 months. Why didn't you just make a new thread?

IIRC, download the MasterMod version of Nintendont, and replace that with your current version of Nintendont. Also, set Nintendont to be your default GC loader.