I recently installed several emulators on my DSTwo card and found that several of them were not working.
So I did some experimenting and this is what I found. (I've edited this post so that it is no longer a question, but a relay of information I found.)
Tested on New 3DS, Old 3DS, DS lite.
New 3DS and Old 3DS worked identical, no issues.
DS Lite will ONLY work if you use a 32 gb microsd card or smaller. My DS wouldn't recognize the DSTwo with a 64 gb card.
(I've actually only tested with 64 and 16 gb, but based on other posts the limit appears to be 32.)
Non-DSTwo exclusive emulators such as nesDS, nesterDS, and snesDS did not work out of the box from the collection of DSTwo emulators.
Why? The downloads only included the "_dstwoplug" files (*.bmp, *.ini) for these emulators to run. I had to find and download the actual emulators (*.nds) and place them in the _dstwoplug folder as well.
DSTwo exclusive emulators did not work at all. They would just go to two white screens, top and bottom.
Why? I was using a 64 gb microsd card. When I switched to a 16 gb, everything worked fine.
NOTE: NDS games boot up fine from a 64 gb card, but emulators do not!
I've confirmed that DSTwo save states function also works. The game guide and cheat system probably work as well, but I haven't tested them.
I am using latest DSTWO Firmware v1.25 eng and dstwo patch 2012_12_6
In summary, 32 gb or smaller micro sd have all functionality across all systems. Larger than 32 gb cards appear to only work with the 3DS family and exclude emulator support.
Does firmware make a difference? Or the patch? Any other useful information is welcome. I hope if anyone else has my issue they can find this post and save themselves a lot of headache