new edit: It appears that this update is only for the GMP-Z003 version of the M3i Zero cart. The older version will not work with this update. It is currently unknown whether or not the M3 team is working on a fix for this issue.
edit: I have confirmed this update to not work on the current version of 3DS and DSi so don't update yet. It looks like they have not officially posted the update on their main page yet.
The M3i Zero has been updated to correspond with the latest 3DS firmware update to restore compatibility.
Straight from the official M3i Zero home page:
M3i Zero GMP-Z003 Firmware Download for 3DS v3.0.0-5&DSi v1.4.3 has been released. 10-12-2011
Update the firmware of the M3i Zero GMP-Z003 card to support running in new 3DS (Ver. 3.0.0-5E, Ver. 3.0.0-5J, Ver. 3.0.0-5U) and DSi (Ver 1.4.3E, Ver 1.4.3J, Ver 1.4.3U, Ver 1.4.4C) system version.