Do you have another sd to try?
I have two, the original toshiba 4g and a cheap officeone 16g.
Both are class 4, needless to say the 3ds is only rated at class 6 and the new 3ds class 10, non do uhs so don't fork out for a class 10 uhs 3 unless you are using it on other devices.
The toshiba never fails to boot. The officeone varies.
Sometimes the lower screen sticks on the flicker before the 'hold r' prompt or anything for that matter on the top screen. It just freezes with a pixulated lower and black top.
Other time both screens blackout and freeze after the lower screen says loading xxxxx.dat.
Other times i get the top screen 'hold r' prompt but both black out soon after regardless if i press r or not. Just tried it then and i average 1 out of 5 successful boot.
Both have the same files and the original never fails.
I don't know of thats your issue, just throwing it out there in case. I hope you sort it out....