Now this is interesting. I have had similar problems over the last few weeks. I assumed that it was my IR extender playing up. Eventually (this weekend) I couldn't send any IR codes at all, which supported my hypothesis, so I shipped the extender back to Laser.

Before it packed up altogether, the symptoms were similar to yours, but not identical. I didn't lose any codes completely (including a Pioneer plasma), but some became intermittant. Especially macros set up to do multiple kit power up/down. So I'd end up switching off the receiver and the satellite but not the plasma, or the plasma and the satellite but not the receiver. Seemed to be worse for the first command after IPAQ power up.

Unfortunately, I'm at work so I don'ty have the IPAQ with me, I think it's a 3850, and I did a PPC software upgrade about a month ago.