An excellent test. If a VPN makes something faster, despite the fact that it adds overhead to the process, that seems like proof that it's being throttled.
Not necessarily. It might just be bypassing the congested route that everyone else on your ISP is using. Comcast and Verizon have had disagreements peering with Cogent, one of Netflix's ISPs:
It's not throttling, but rather the peering points along the "best" route between Cogent and Comcast/Verizon are overloaded, resulting in lousy connections between them. Look at this traceroute hop from Comcast to Cogent I just recorded:
7 he-0-10-0-1-pe03.111eighthave.ny.ibone.comcast.net (68.86.83.94) 21.377 ms 20.379 ms 19.387 ms
8 be7922.ccr21.jfk10.atlas.cogentco.com (154.54.13.161) 67.126 ms 67.747 ms 69.083 ms
40 ms to go one short hop in, I believe, the same data center.
It's not being throttled. There is a peering dispute between netflix's CDNs and the ISPs. Netflix's CDN's don't want to pay for delivery to the ISP. Normally CDNs peer with each other for free if the balance in each direction is equal. The problem is that any CDN that delivers netflix is hugely unequal since it's a huge one way stream.
The ISPs could just eat the cost, and let it be delivered for free. Or Netflix's CDNs could just pay the peering fee. Or Netflix could use different CDNs.
The reason the VPN works is because it sends the data over a different CDN that isn't saturated because of the dispute.
At least that is how I understand it, but I'm not an expert (or even a novice).
Umm wait, isn't such a dispute exactly what we call net-neutrality? Consumers pay ISPs for internet access, and now ISPs also want money from websites that provide a service to the consumers. But filtering those websites until they pay the ISP to be let through is the opposite of net neutrality. If what you're saying is true and ISPs are asking Netflix (or subsidiaries) to pay them to be let through unthrottled, then this is indeed the net neutrality problem as the OP reports.
Edit: Wait I think I understand. I messed up peering and ISPs, right? Because the CDN connects to the internet via peering, and they're charging money (which does make sense to me), not the ISPs.
Oh, and the even more galling part... when watching Hulu on regular Comcast (without the VPN), the shows average around 500-900kbps. When it flips over to displaying the commercials, it jumps to 8Mbps or more!
This is actually not malicious at all. An individual ad gets served to many more people than any given show, and as a result they'll get cached closer to the destination. Still pretty obnoxious though :)