I also get the "go to website to update the remote" error about a third of the time. I figured out the problem (at least with my setup).
I have the Harmony software set to "watch the download folder" so that after the hex file is downloaded to the computer, the harmony software will automatically upload the data to the remote. For some reason, I believe the software tries to upload the data to the remote before the file is fully downloaded to the computer.
After the upload fails with the "go back to the website" error (which I'm guessing is a generic way of saying "the upload did not successfully complete, please try again"), simply double-clicking on the fully-downloaded data file on my desktop always results in a successful update of the remote.
I can tell if the automatic upload is going to fail, because the "thermometer bar" that measures the upload of the data to the remote goes much faster than what you see if the upload is successful.
Since this "upload failed" issue didn't crop up until near the end of my initial configuration of the remote (probably 40 uploads over a span of two days), if I was a gambling man, I'ld guess the problem has some relation to the downloaded data's file size.
I started remote configuration by listing every component I had on the website and after spending more than a short while drowning in the bazillion options offered by the website when selecting the "let me show you all actions available for your group of components", I deleted everything except the TV and the A/V receiver. Then I always selected the "let me add the Actions I desire manually" option and started to slowly add the specific actions I wanted. This way I had a much better idea of what to do and how to go about it when later adding additional devices one at a time (TiVo, Cable DVR, DVD player, etc.) and adding Actions that pertain to those devices.
Since I didn't get the "please go to the website to update the remote error" until after I had added numerous components and configurations*, I'm guessing the downloaded file size got to a point that it triggered something on my end so that the upload to the remote started before the file was fully download. The first thing I would test is if my automatic anti-virus scan of downloaded files, even though quick on such a small file, is somehow gumming up the works by introducing some sort of delay between the time the file is fully download and the time that it is "ready" to be uploaded. Perhaps this delay is confusing the Harmony software update process.
But I haven't tested this because the problem didn't occur until almost the end of my configuration process and now that I'm rarely updating the remote anymore, there is no annoyance. And since I can just turn off the Harmony software "watch for downloaded files" option and start the remote update manually by double-clicking the downloaded hex file, it's just not a bother anymore.
I can also confirm the high WAF -- after getting the remote mostly configured, I presented it to her as the gift of being able to actually use the home theater system in the living room (i.e., listen to FM and CDs). My lovely bride narrowed her eyes and said "and how much did this cost?" Five minutes later she was saying, "well, this is cool" and "that HELP feature is very nice" and "so we can program in the buttons for my favorite radio stations?"
*I could try removing the photos from the slide show to reduce the downloaded file size -- it's possible that the update error began around the time I added them. Perhaps it is as guessed simply a matter of download files size, perhaps it is more specifically related to having photos in the configuration.