Ok first - I have already changed the delays to their lowest settings. In fact I have systematically tried them at various settings in hope of finding a "magic" delay that works. No luck.

So here is the story. I've had this 659 for several years and it has been great. This summer I did a firmware update and around the same time Tivo made a major software update to their systems. I am fully aware that the Tivo software is slower than previous releases, but this is not the problem. If I use the Tivo remote it is plenty fast even with Tivo's new "slower" version of software. When using the 659 the response time of the Tivo is painfully slow. I would say 3 -4 times slower. It wasn't always this way.

I feel like something is not right with my 659, but I have no way of determining what that might be. My guess would be a firmware issue, but I have reinstalled firmware several times and there is no change. According to Harmony there is no way to return to a factory default state.

Any suggestions?

Have you tried reducing the number of times an IR command is sent (the default is usually 3)? This setting is hidden away in the troubleshooting section:

"Troubleshoot" ->
"Show me more problems" ->
"Device doesn't appear to receive every command correctly." ->
"The device responds too much to some commands"

Thanks I tried it, but it didn't help. Even tried another firmware update to no avail.

I dunno.

Try "Confirm infrared commands" (under Device > More Options).

Just finished trying "confirm infrared commands". It -might- have sped up the Series 2 Tivo, but still not anywhere near as fast as the factory remote. Thanks for the advice folks.