First of all, I need to commend you for bringing us such detailed information. I really appreciate what you have done here.
Are you dual-booting your box (meaning, are you using the same machine when you are doing this test)? There are three possible areas we could criticize here:
Windows OS
Hardware
Drivers
The Windows OS could have some hardware or driver related options that could interfere here (I wonder if XP would have the same issue here).
Maybe the hardware or cable is picking up on some secondary hum (this theory sounds good in my head)… but I would like to see if you are using the same machine for your purposes.
We can also try and use older drivers to see if that will take care of the spikes.
More I test the less I understand :
For my firsts tests, I’ve tested on a Dell laptop with :
Windows 7 Pro x64
Ubuntu 12.04 x64
Windows 7 Pro x64 in virtualbox under Ubuntu.
On Linux it’s OK, on both Windows I’ve the strange signal.
On a desktop computer with Windows 7 Ultimate x64 it’s OK.
I’ve installed a fresh Windows 7 Pro x64 on my virtualbox and it’s OK.
I think the problem must be a software or a driver on my install.
Thank you for following up and sharing the solution to this problem! It is strange that a program like this is polling the USB ports every so often, but that explains the regular spikes. I wish we could have a nice oscilloscope like you do because there is no way we could recreate this or analyze the output like you can. That is why I am glad this could be solved by the process of elimination. Thanks again for all your information.