I having problems getting STP on two stacked 3500XL with 1 Gb link to a 4006 Cat to shutdown one of the two links. Works fine on a single 3500XL with two uplinks.
I am a little out of my element on the LAN side of things so forgive me if this sounds silly. Are both of your 3500XLs entireley in the same VLAN? Because each VLAN runs its own instance of STP. Are you seeing loops as a result of both ports being open?
Why would you want one too be blocking. STP takes the best path back to the core switch. Obviously for each of the 3500's the best route is to use the gigabit uplink back to the core. One of the interfaces should be blocking on the gigastack links. If one of the Gigabit uplinks were to go down, STP would recalculate and all of the traffic would then go out the remaining uplink.
What it sounds like is happening is that STP is blocking the link between the 2 GBIC's. I have seen this before on my network, the path through the GBIC is one hop more than your link back to your 4000.
