I have a very simliar issue! but with load balancing added in...

3900 -> 2860

3900: 192.168.3.0 (PRIMARY) AND 192.168.6.0 (ADDITONAL)
2860: 192.168.2.0 (primary) and 192.168.7.0 (additional)

SIngle VPN setup, without GRE and all work ie from can ping both subnets at opposite end of the trunk.

With GRE and load balance, Can only ping from primary to primary

Routing tables look OK...

3900
10 192.168.7.0 (Gateway IP) 255.255.255.0 UG 0 wan-wan2

2860
S~ 192.168.3.0/ 255.255.255.0 via [GW Address] VPN-3
S~ 192.168.6.0/ 255.255.255.0 via [GW Address] VPN-3

Do I need two tunnels, and if so how do I set that up at the 2860 end??

THanks for any help/advice!

Alistair