Hi,
Some observations:
1. The EX is now root bridge for all the instances except vlan100 [Root ID and Bridge ID being same]. As a result, since the EX is now root bridge, all the ports will be in Forwarding/Unblocked state.
There has certainly been STP topology change in the network.
2. The EX seems to be connected to another switch on port xe-5/1/0 [Root port for vlan100].
Don't know what your config is like so can't really say what happened when you removed vlan1 from the trunk.
Did you configure vstp as "set protocol vstp vlan all"?