Hi Ivan,
Most non-EXOS switches (and I assume the Ruggedcom switches behave this way as well) will send BPDUs untagged regardless of the vlan tagging on a port. In EXOS, there must be a carrier vlan defined for an STP domain, and the the tagged-ness of this VLAN determines how the BPDUs will be sent (IE, if the vlan is tagged on a port, the BPDUs will be sent out tagged for this vlan).
Because of this, if you need to interoperate with a switch that always sends its BPDUs untagged, there will need to be an untagged VLAN on the ports in the STP domain. You can either have an untagged native vlan on both sides of the links, or simply add an untagged vlan on the EXOS switch purely to handle the BPDUs.
Let me know if anything wasn't clear, it can be a bit confusing.
-Brandon