I'm using the latest TOR bundle, I am able to connect to the TOR network and able to load www sites thru TOR but for some unknown reason not able to load onion sites. However if I connect to TOR inside a VPN tunnel I am able to load onion sites. Could it be my ISP is somehow intercepting my TOR connection?
Everything to your entry guards is encrypted. I can't imagine that there's any observable difference between "you<->guard" traffic for regular websites vs hidden services.