A novel robust watermarking methodology for intellectual property core protection of control data flow graphs during behavioural synthesis based on user specified resource constraints and loop unrolling factor is proposed. The proposed methodology incorporates robust multi-variable signature encoding scheme for securing against typical attacks such as false claim of ownership and tampering. Some of the features of the watermarking include greater robustness, lower embedding cost, lower storage overhead, fault tolerance and faster encoding/decoding. Experimental results suggest that the watermarked solution generated by the proposed approach produces lower embedding cost than previous approaches, as well as is more secured due to its multi-variable signature encoding rules.