Can Raptorcache work on a transparant bridge?

[WinH]

My setup is like this: <>

WIN7-PC <> RAPTORCACHE <> NAT-ROUTER <> INTERNET
-------192.168.1.0/24-------192.168.1.1-----PUBLIC IP

The Raptorcache machine has 2x NICs eth0 and eth1 which are bridged to br0.
This setup has always been working fine with just Squid as a transparent bridge.
(for example like this http://freecode.com/articles/configuring-a-transparent-proxywebcache-in-a-bridge-using-squid-and-ebtables)
Now this server has been reinstalled with the RaptorCache solution and everything seems to be working but I have some strange problems with Windows Updates failing and YouTube only works in Chrome.

So my question is, can this be because I am running in transparant bridge mode?
Does raptorcache do any kind packet sniffing on eth0 for extra intelligence or does it only work on application layer together with squid cache peering?