What all files do you have on the root of the Micro SD card? I ask because you should only have the update to 1.4 files for either the DSi or DSLite on there. You can have both and choose but I just put the DSi on mine since I was only doing one card. If you have the system files on there too then that may be your issue, if you do not and you just have the update files on there then you may want to try using just the one update file at a time and see if that helps. If that fails then you could have a bad card or you could have corrupted the card. It can happen, there is a warning about it in the updating section on 1.4 for Acekard, though that is unlikely as it rarely happens. Anyways if it is still happening I suggest trying another DSLite unit to make sure it is not a problem with the unit you are using. If that fails then you are out of my league and will have to get help from someone with more expertise in the matter. Hope this helps at least a little. Sorry to hear about your issue. Best of luck to you.
Sincerely,
Elmoreas