AH HA! My suspicions have been confirmed, or at least had more evidence supplied to support them further. I too was having a delay problem with the SA8300HD, but it was almost "random" in that some of the buttons were immediate and some of the buttons had a significant delay. And by delay I mean the light on the remote (I have a Harmony 676) stayed on for a while then the command would finally take. Unfortunately this primarily affected my number keys. What was really driving me nuts was that almost all of the LCD softkey commands were immediate, and even some of the hard keys were immediate (mostly the play / pause / etc type buttons). So messing with the interkey delay didn't do anything since that green light staying on was my problem really. So I adjusted the command repeat down to 0, but that didn't help. No real surprise there as the green light wasn't staying on for *all* buttons.
Then finally I went to my "nah, this shouldn't make a difference but you never know" plan. A little backstory first; I had a 8000HD that died and just swapped for a 8300HD. The commands all worked and were very quick with the 8000HD and since they use the same remote everything was working fine with the 8300HD when I tried. But I felt I should sync everything up just for the heck of it. So when I went to add the 8300HD I noticed I could add it as a Channel Decoder or Video Recorder. I initially set it up through the Video Recorder path as that has "PVR" listed in the sample devices. Everything worked, but some of the keys had that long send. So ultimately I installed it starting down the Channel Decoder path and now *all* keys are fast! Both modes control the box just fine, but the Channel Decoder instance doesn't seem to have the long send problem.
Way back when I had to add some custom commands for other devices I have I remember reading on the Harmony site that you should use the on-site commands when possible as they are optimized for the remote. The learned commands apparently aren't as compressible / normalizable / optimizable / etc. Now I'm wondering if there's some degree of "corruption" in the Video Recorder instance of the 8300 that has non-compressed commands (or something along those lines) for certain keys (#s, OK/Select, Info, in my case).
One last note, the Channel Decoder path ends up with "Scientific Atlanta PVR (SA8300HD)" whereas the Video Recorder path gives you "Scientific Atlanta PVR (Explorer 8300HD)". I typed "8300HD" into the box both times when it asked me to describe my equipment.