I am having trouble with Quagga in setting up IPv6 BGP. So far it was failing with external providers. Just now I gave it a try to setup BGP session (IPv6 only) within our ASN between two routers.
From our other end router I see there is no acconcement, while I see blocks being announced via Quagga. Also strange enough is that the number of blocks I account - they all come as "withdrawl routes" on other router as soon as Quagga is turned on.
I recall some issues with the value of the next-hop in the BGP messages in the past. Haven't been around Quagga in recent times, don't know if this is still the case. If possible you might want to catch a BGP packet with tcpdump and verify the value in there makes sense to the other side. Got bitten by this before and took me ages to figure out the other side was dropping my updates because the next-hop couldn't be resolved. Marco