Cisco Switching/Routing :: 3750 - Losing Connection With Etherchannel

We have a new building where we added 3 network closets with 3750x stacks.We have 2 fiber gig ports connected to 2 microwave units and etherchanneled the to ports
 
We have the same setup at the corporate office except the connection is 2 fiber gig ports on a 6509. The 6509 is doing the routing
 
Now the problem is that we lost the connection to the management interface on only one of the three closets after a few days running. But some workstations at the corp office could reach it... others could not. The workstation were on the same VLAN. We solved the problem for a few days by shutting on of the fiber ports on the etherchannel. But is started happening again... now with PCs being installed at the new location.
 
The PC that was not working on the 3750x side could ping across to the 6509 but no further then that. It seems like an arp issue not routing because some devices are reachable and fully operational throughout the network.
 
Here is the configuration:
 
3750x:Cisco IOS Software, Version 12.2(55)SE1 
Current configuration : 118 bytes!interface Port-channel1switchport trunk encapsulation dot1qswitchport mode trunkno snmp trap link-statusend
!interface GigabitEthernet1/1/1description 2gig to STB-6509switchport trunk

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