I think the reason M-audio suggests using the supplied card is there are NO ISSUES with the protocol on the supplied card, but there may be some incompatibilities with protocols on some other types of CF cards faulting the upgrade process, especially the 'super-speed' types. Card capacity seems not the issue.
If you've lost having the supplied card, choose a 'slower' CF card, and format this card in the deck BEFORE transferring the three upgrade files to that card either using direct-to-deck USB connection, or card reader attached to the computer. Then upgrading should go smoothly.
I couldn't find my supplied card, so chose 128 MEG Sandisk that's been around for 5-6 years for photo purposes, formatted in the deck, and direct connected the deck to XP computer that recognized it as external storage device.
Transferred the upgrade files, disconnected the deck, turned it off/on, and used the menu to choose UPGRADE FIRMWARE. Deck upgraded, then rebooted to show correct 1.05 boot-loader and firmware update.
Now to go out to record something with my Ultra II 8 GIG (never had an issue using this card in MT) confirming no downsides to newest 1.4.6.
Interested in postings of at least new issues appearing with 1.4.6 update, and if past issues with other makes/model types of CF cards are consistently resolved.