Hi bstaber,
I know this has been a persistant issue for you so I will try and shed some light on the situation. When you are using the old harmony member website, you are actually downloading the "update" file manually. Although the same information is being transferred into your remote, the Harmony software and the old member website access this information differently.
Due to this difference, if there is some security blocking the Harmony software, you may still be able to update using the old members site.
If you refer back to your logfile posted in your original thread, the last entry shows that uploading information was successful.
__________________________________________________
Uploading remote control information to web - Successful
Finished
_________________________________________________
Bascially this means the Harmony software has detected your remote and is attempting to begin the update (uploaded info to web). This brings your update percentage to 3%. The software is now waiting for information back, but until it is received, the software now hangs at 3%.
*If the update were to proceed past 3%, the next thing displayed in the update log should be something like:
_________________________________________________
Uploading remote control information to web - Successful
Finished
Starting communication
Starting communication - Successful
Estimating time to update remote control.....
_________________________________________________
I saw that you have tried disabling all security software, stopping services, different USB cables, tried safemode w/ networking, and 4 PC's. I am very surprised that the update still does not go through. This would seem to indicate that your security software or OS is not at fault. You mentioned that you also have a D-Link router. Did you try connecting your computer directly to the modem? By bypassing the router, this will tell you right away if the router is affecting the update. If this works, the router may need to be configured to allow access for the Harmony software.
The only last explanation could be your ISP (Internet Service Provider). Depending on your ISP, there may be network restrictions or some type of filtering, out of your control, which affects the Harmony software.
As a suggestion, you may want to try updating your remote on a completely different network. This could be a family member, friend, or work computer (although some companies also have network security) or anywhere else. If you are able to update your remote successfully with the Harmony software, then you will know concretely this was network related.
The bottom line is that you have now been able
to update your remote successfully. I am truly sorry that this has been
so dissapointing for you. For the majority of Harmony users, the remote
software updates without any trouble at all. I'm sure you were excited
to use your new Harmony remote and I am glad you have finally been able
to update. I hope that you can start to enjoy it 
Regards,
Mark
