One very common issue running tunnels and routing protocol is learning the tunnel end point via the tunnel. This will cause the adjacencies to flap. The tunnel is also most likely going up and down but you will not see it since tunnels like to lie and say they are UP/UP.

First turn on the tunnel keep alives with a very low value and make sure they are stable before you activate EIGRP.

The other thing you can look at is MTU size on the tunnel. I don't know if this effects EIGRP too much I know OSPF has issues.