Just make sure that in the properties section (General tab) of each individual CD, the titles are identical. Also that "Part of multiple disc set" shows 1/2 for CD1, and 2/2 for CD2.

For those doubles that tell you they are already part of a set, simply highlight the relevant discs, go to the 'Tools' menu, and click on "Unmake box set". Then follow the instructions I gave at the start.

Hope this helps!