Also having same problem. Downgraded N3DS to 9.2. Removed menuhax before cloning sysnand to emunand. 9.2 emunand works fine using ReiNand and CakesFW. When updating to anything else (9.9 using game cart update, 10.3 using files, 10.4 using internet), I get the "starting home menu" popup before going to black screen. Have to restore emunand backup to 9.2 before it works again. May be worth noting when holding power button when semi-bricked in emunand, it shows the sleep/power off message. Not sure if it's problem with sd card files, incomplete update or something else?
EDIT: Got it working! Used the link @
Anotherply posted above and deleted the 00..008f folder and it went back to "starting home menu" after updating. This time it was actually creating it and loaded to home screen. Just tried 9.9, gonna try 10.4 now.
EDIT2: I think another thing that may have solved the problem this time was deleting cia titles I installed on SD and NAND from before. Apparently formatting system does not wipe those out as I tried several times but it still appeared when checking through FBI.