Hi Robbie,
I guess the BUM (broadcast/unknown unicast) traffic on your trunk exceeds the 1Mbps limit you set. As discussed in some other threads, the is no single correct bandwidth value to configure in all networks.
You should look at your network (sniff the traffic in each VLAN) to verify what's the 'regular' BUM traffic level or why it's so big. Depending on network size & applications 1Mbps may be OK.
Unfortunately Junos does not reported what BUM traffic level triggered the storm-control and I'm not aware of any easy method to measure unknown unicast level (without sniffer).
Test the config with bigger bandwidth values for trunk port.
jtb