You want to configure your vlans, and assign the vlans to the specific port/port-channels prior to enabling a port that has a connection. The designated receiver role for a given vlan will get chosen from the available logical uplinks, and if that includes your connection to no where (as far as that vlan is concerned) because you haven't pruned off the vlans, your ARP and broadcasts will no longer function.
You have a 50/50 chance (for 2 logical uplinks) that the uplink chosen for a given vlan's DR will be correct.
We frequently see customers with incorrect disjoint layer 2 configs that worked for a while, whose issues didn't show up until the ports were flapped, at which point the vlan(s) DR role was reevaluated and assigned to an unintended port.
Kirk...