The only other thing I can think of is a bad rxTools build. I'm actually not very familiar with all the different Nightlies in terms of "what works on N3DS/O3DS, which is the best for you..." so all I can say is "try different builds of rxTools, or resort to CakesCFW."
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OH wait a second. Maybe you have menuhax on your emunand. Try holding your menuhax button as you're booting emunand and see if you get in. Change the theme if you do (make sure nands are unlinked first though)