I'm not familiar with BlueKenue, but here some hints to verify if your boundary conditions file is relevant with your geometry file.
1- verify that boundary nodes number is equal to the number of lines in your BC file
2- If you are using different tools to generate your model, verify that you have the same numbering. This could be done easily by choosing randomly few nodes and see if they have the right coodinates, if they are really boundary nodes.
3- For Janet mesher, the numbering starts from 0, for Matisse, it begin from 1, for BlueKenue I don't know, try to verify!
4- If you are using fudaa, and if you can load your geometry file correctly, you can generate a BC file correctly, Janet do that also. So try to load your geometry file generated by blueKenue directly by fudaa, generate a BC file and use it in stead of the one generated by bluekenue.
Good luck
Riadh