Very strange. I've literally just updated my own Acekard 2i with that file (also ran it through my old DS Lite to update it like you did) and it now working perfectly on both my DS Lite and my 3DS which has the latest official 3DS firmware installed on it. The Acekard shows up as 'Deep Labyrinth', doesn't say it's the (European Version) but don't think that matters.
Couple of suggestions, What's the 'HWID' number of your card? Apparently (according to the readme.txt file, if your Acekard's HWID number is 44, the update won't work properly...you find the HWID number by booting up the Acekard, pressing start and then selecting 'help'...although if you bought your Acekard after February 2009, you should be fine)
Other than that, I'd try maybe flashing an older version of the Acekard firmware onto your Acekard and then reflashing back to the latest one. And also before you do anything else, try backing up all your files, reformatting your micro SD card (with Panasonic SD card formatter) and starting from scratch.
It really should be working OK on your 3DS (as I said, just done it myself with no problems).