I also teak the min repetitions to the minimum that will work reliably, and often it is 0. This makes for shorter transmit times and less chance of interference in long macros. The test button in the Edit mode of the librarian is excellent to try codes and tweak very quickly.
For reliable capture you need to set the two remotes on a table and find the best position with both remote IR sensor/emitter windows level and parallel. In a couple of instances I had to raise one or the other with some padding. Also make sure they are stable when you press the buttons in the different locations of the "donor" so it won't wobble. I had problems with the Hughes HDR-205 DVHS recorder at first until I made a process out of it, then had 100% reliable capture.
On the other hand, I cannot get even a reading from the TA-E9000ES remote :-(. Fortunately I was able to transfer them from ProntoEdit with the "hidden" hex code editor. I hope they can do something about this.
Other than that, this remote is a dream come true.