Sounds like you haven't actually installed A9LH yet if it boots without the card. So, you can't get Menuhax to come up? If that's the case, just put your card back in after turning the system on, and change your theme. Then reinstall Menuhax. Of course, from what I'm reading Browserhax is down atm, so, you may have to wait for that to come back up if you aren't using an exploitable cart. EDIT: Just checked it, seems to be up now.
That said, I once had a large card that hated running payloads from a boot manager for some odd reason (maybe BootCTR was too fast for it). It would run one payload, then trying to boot anything but HB menu gave me a black screen until I reinstalled Menuhax. Running them from the HB menu solved the problem until I got A9LH up and running. Probably some junk clone card.
I would use TinyFormat. Keeps your NNID intact, and anything installed to NAND (including legit DSiWare). You can install NAND DevMenu, for example, then run TinyFormat, and it will still be there (highly recommended). But I would be certain they're linked. Try installing something in each. See which folder it goes to each time. CN is small.
I was about to ask if you had MicroSD Management installed. The old versions do that. There are decrypted versions that fix the problem. Do a search for "microsd management" on a certain iso site. Second thread.