That's definitely real. Normal, unobfuscated VPN will result in packet drops after a couple of minutes. Even obfuscated VPN will trigger packet drops if you send too much traffic.
It depends on the protocol. Unobfuscated OpenVPN definitely behaves in the way you describe. But I very rarely have problems with PPTP, which is unobfuscated.
Put simply, AFAIU, it's the pattern of TCP packet sizes. OpenVPN, for example, has a very recognizable handshake that makes it prone to detection. This post goes into some of the network-level details (not OpenVPN-specific): http://blog.zorinaq.com/my-experience-with-the-great-firewal...