The MX990 firmware would have updated when they downloaded their program to the remote.
[edit]: Just realized you were probably talking about the JVC projector.

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Something you may want to try, switch the JVC projector to respond to the other code set (as Daniel described above); [also make sure the firmware on the projector is up to date - see above]. It could be the code set JVC is publishing, is actually the B code set. Despite the fact they are saying it is the A code set - it happens.
I remember a long time ago, some Sony A/V receivers would come setup to respond to alternate code sets (1 of 3 if I remember correctly) and I would have to either switch the receiver or use an odd database set.