Hi,
First of all I must say I was wrong in that it wasn't true that the server was available on some ports and not on others (80 and 443), it couldn't be reached on any port.
I have found that this is a problem in the routing in the second context. I have a generic static route pointing at 10/8 through the gateway and one loadbalancing service defined with this server in this context (linked to a policy-map with a class-default and a forward action).
The issue is that with the A1_6_3 IOS version the generic static route 10/8 works fine for the traffic destined to this server, but with the A2_1_3 IOS version the ACE doesn't know where to forward the traffic (I guess it is a bug and the fact that this server has one service configured makes its ip known to the ACE in some way that generates a conflict in the routing decision).
I have overcome the issue by installing a static host route pointing to the server with the same next-hop the 10/8 route has.
Hope this helps someone when upgrading the ACE.
Thanks&Regards