Always remember, if the native VLAN is different from VLAN1 then:
1. VLAN1 standard STP BPDU is sent untagged
2. VLAN1 PVST+ BPDU is sent tagged with VLAN1
3. Other VLAN's PVST+ BPDUs are sent tagged accordingly (the one for the native VLAN will be untagged).
Then, tell us what is the native vlan on your trunk and what STP flavor are you using?