So it's a power supply issue to the flash card. I didn't consider that before having the region switch installed on my Duo-R.
Flashcards a fickle when it comes to power consumption. Most region mods tell you to take 5V near the cartridge slot. It'll work fine for original HuCards, but with flashcards, any interruption of power (power drop caused by the 5V taken from around/at the HuCard slot or the length of wire for the 8PDT switch) will cause the flash card to not work.
Depending on what mod chip is installed in the Duo-R, you could just get power directly from the 7805; if it's the 4551 IC, more voltage won't hurt it (4551s can take up to 18v) so you can use the input left, the main IC on the "Obey" chip max voltage is 7V, so get power from the right leg. If it's the 8PDT, just remove it.
...just my observation regarding Everdrives and region mods.
THAT BEING SAID, Sifu, if you're not gonna worry about getting original HuCards, then you won't need to region mod it. Done.