Easy enough to tell - get a list of what interfaces are associated with vlan "default" (vlan-id = 1). Do you know what interfaces blocked previously? Those links should NOT be trunks (port-mode = trunk) but should be access associated with just the 1 'routed' VLAN. Therefore, native-vlan-id would not apply.
There is obviously something wrong, just need to figure it out. Mostly config is in error.
Why not just open an work a JTAC case for this?