When I push the channel up button it goes along as it should for a bit, then for no reason when I press it, it will go to a channel out of sequence. E.g., if I'm on channel 9, then press the channel up, it will go to channel 22. It puts out numbers that don't make sense.

Also, some of the channels in the guide don't work. E.g., if in the favorite list I have channel 39, and I select it, nothing happens. The direct channel entry (using numbers) doesn't work right either.

I really like the idea of this remote, but it's getting bit frustrating to get it working properly.

I agree. I love almost all the remote's features... including the ease by which my wife understood it. BUT!! I am very frustrated with the channel listing. My problem is that the list on Harmony's web site doesn't match the channels (recently - 6 months ago - updated by my cable provider). So, no matter how many times I try to tell it that HBO lives at channel 400, NOT 100... it just won't believe me. I went over to the Zap2it web site (which powers that section of Harmony) and the channels looked fine!

NuYawka,
Have you tried editing the XML for the channel numbers? I have reordered the channel numbers by modifying the XML however, I haven't tried replacing a channel number. However, if you want to try it,
Click on My Activities.
Click on Modify the XML...
Click on the Cable Box Activity
The XML will be displayed.
Find HBO channel 400 in the XML and change to 100. Save changes and download to your remote and test. This is only a temporary fix because the next time your remote is updated the channel number will probably be overwritten. However, maybe the guide will be updated by then. You may also be able to add the channel manually when selecting what channels are hidden and the favorites. I know there is a tab to allow adding a channel.
Hope this helps!

Another Suggestion...
Nuke all of the channels by selecting some local cable company's basic list, and marking them all hidden.
Set number of days to 'O'

Then add two change button function activies that re-map the FeatureUp/FeatureDown buttons (internal name for channel up/down) to send the IR command for ChannelUp / ChannelDown.

The change button function activities are specific to your configured activies and devices. As an example you could apply the mapping listed above to the 'browse all' menu under 'WatchTV' and have the IR commands sent to your TV. In effect this transfers the "keeper of the scan list" duties from the Harmony to the TV.

If you are happy with the channel scan list in your TV this should work fine. You may want to autoscan channels on the TV to get 'em all in there.

If any of the numbers turn up incorrect in your channels, you can easily modify them on the EasyZapper site. Just go there and follow the directions.

Further, if it is changing Up and Down incorrectly, this suggests the remote setup was not quite complete. Either try again, or ask their tech guys for a quick hint. They know this topic inside and out. ... Mike