Just to make sure: yours is a O3DS? N3DS only support 9.5 EMUNAND.
If O3DS, I don't think it's the memory card. I installed EMUNAND for a friend on stock 4GB memory card, works just fine. I even re-created EMUNAND (after I asked if there is a way to format setting setting on EMUNAND if @Shadow#1 can remmeber) just couple days ago and updated to 10.2 just fine.
That's being said, try with other SD card.
By any chance, your NANDs are linked? If so, you need to unlink the NANDs if you want EMUNAND on a different firmware from SYSNAND; and booting using Themehax.
Yes I am on O3DS xl. May I ask which version of rxtool and GW ultra did you use? Could it be possible that it has something to do with the files I used? Before I try it on a different SD card, I would like to know which rxtool and GW ultra should I use for my 6.x O3DS.
Thank you very much.