This looks like the problems I had with the first TSU3000 I worked with, but with a twist that might help. I had codes in the long form, learned with a TS1000. When I copied and pasted them into the 3000, they came out as the short form after closing the edit window and reopening it. Have you checked with the above long codes to see if your remote is changing them to the short form? There might be something wrong with that process, and from the posts I've read it's likely to be a duration issue. I never did figure out what was wrong with the TSU3000 -- we changed remotes.

Also, there are three varieties of learners that I've had ZERO problems with: the Crestron, the RTI, and any TS1000/TSU2000/TSU6000. Carry a TS1000 with you for cases like this. You'll be able to learn codes and test them much more easily than you can with the Crestron or RTI learner.