Channelk,
I think you should reinstall all your Line 6 Drivers. I don't think the driver behavior while installing were ok at all.
If I were you, I'd reinstall both drivers and Line 6 Updater, reboot the computer and test if there's conectivity between Helix and your PC.
After that, try to reinstall the update.
I myself did the ONLINE update, and it worked fine. I did it as follows (even thou there was no instructions to do that):
1 - Downloaded the latest drivers;
2 - Installed the latest drivers;
3 - Download the latest Helix Editor;
4 - Installed the latest Helix Editor;
5 - Backedup all my patches;
6 - Turned off Helix, turned on Helix and did a Global Settings RESET before update (don't ask me why, but I did it);
7 - Followed the instructions on Helix update page for ONLINE update;
---- That is one information that I think should be very useful to you...
Some USA A/B cables have a "filter" that stands near one of the ends (they're mostly in a cilyndric shape) and I found it to be giving me problems while updating my past POD HD 500x. I then tried to update the POD HD with a normal cable, without the filter and everything went well. Maybe you should look if is there any filter in the cable you're using.
(Sorry for my english writing as I'm a portuguese native speaker! I don't know if I explained it right)...
Regards,