Hacking Sky3DS or Diskwriter Issue

[scyther3989]

I have an issue with the diskwriter or my Card. I'm working with Monster Hunter 4 Ultimate and Pokemon Alpha Sapphire. When I flash a Monster hunter rom and pokemon alpha sapphire rom after in diskwriter it doesn't work. However, if I flash either of these alone it works just fine. If I flash Mh4U then pokemon then mh4u will run. But I can't use the blue button to switch to pokemon and the LED blinks constantly. If I plug it back into the computer it appears corrupted. Then I have to format the sd card before I can do anything else with it. If I write pokemon first then it runs and I can use the blue button to switch to MH4U. But when I do and try and run it, it says unable to read game card.
Is there anything I'm doing wrong?

 

[UsualNoise]

Have you tried a different SD card to rule out a hardware issue?

 

[scyther3989]

Switched out to a 8gb I found lying around. Wrote both games and they work like they should. Thanks for the help