Is it a public or private header ID? IE is it a ROM dump of your personal copy, or a download?
Go get latest Diskwriter and template0310.txt
Go get ROM Patcher v1.1 (export the ROM header to file)
No Ban No Sky (connect header file to template)
Go get Sky Army Knife (very handy if you can get it work)
Time to open up notepad and make sure your template knows your ROM has the right template header.
Open up Diskwriter, CHANGE TEMPLATE to your new one and then try it.
Oh, and don't be shocked if your savedata is corrupted. Especially for EEPROM-NO games. Backing up the savedata of the ROM from Diskwriter doesn't backup the actual 3DS SD card savedata which you now have to match as well. EEPROM-YES games, just use Diskwriter to backup savedata.
I'm guessing this is what's happening:
You wanted to play Animal crossing online so you dumped your private header. You slapped it on the SD and popped it into your Sky3DS. You forgot to change the template header for Sky3DS, so when you put in Sky3DS (you have to do it about x3 times for newly formatted SDs) and everything else displays a menu screen but the one game you didn't match headers on. So Animal Crossing is there, but you get a blank title screen and empty icon.
I've done this when I was playing with template headers.
MATCH YOUR TEMPLATE TO YOUR ROM HEADERS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Doesn't matter what game, but it does matter for using private headers. Porkymonzterz, Super Gay Bros, Animal Crutching... even EEPROMs. If you use private headers you gotta patch the Sky3DS template to use them.
Eventually Sky Army Knife will be awesome as it will combine all the tools into one to make this easier. But for now it's a task to match headers.
Oh, and one more thing, don't use more than 31 games per SD card. Sky3DS isn't really "unlimited".
Let me know how it goes... your Sky3DS is okay. Trust me. It's the freakin' template. Oh you might want to also go get a copy of ROMTOOL v3.1 to trim your roms if you're trying to max out 31 games on a 32GB SD card.