Part of the way WotC handles this is by tracking warnings and penalties through the DCI number/registration that all players use to register for tournaments. If a player accumulates too many warnings, he or she can be disqualified or sanctioned. This helps prevent the "two free cheats" otherwise inherent in the warning system.
The way to handle a disagreement about a face down enchantment is to give both players a "disputed playstate" warning and then track those warnings across tournaments. Everyone will get a few, but cheaters will get more. So will sloppy players, but the system will probably help them tighten up their play, so that may be a feature, not a bug.
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If technical solutions are an option, we might be able to borrow a trick from Warmachine: you can write on gloss card sleeves with a dry erase marker. Just make a dot of the appropriate color on the back of the enchantment's sleeve: red for attack, purple for incantation, etc.
Alternately, records could be kept on pre-printed pads of paper with pre-printed checkboxes for each enchantment.
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If we're feeling really snazzy, we could pre-print those checkboxes right on the back of the card-sleeves.