I had the same issue recently with the MX3000.
It wouldn't learn certain codes. I tried everything.
Finally I tried learnig the codes that wouldn't
take into an old Marantz RC5000i. Voila, no problem.
I then tried learning those newly learned codes
from the RC5000i into the MX3000. It worked like
a charm. I wonder if the URC remotes have a kind
of code filter that rejects certain information
that is percieved somehow as unaceptable. Or,
that the RC50001 has a process that cleans up
the codes. I'm not looking a gift horse in the
mouth here, but I'm curious to know what's going
on in this convoluted process.