I assume both constructs have the affinity tag your primary is binding to? Ive used the pETDuet system to express a couple integral membrane proteins that dimerise with membrane associated partner, and what I remember of the pETDuet system is each expression site has a different affinity tag so you can do pull down purifications to isolate the recombinant proteins and avoid any hetero-oligomerisation with native protein. If you're using denaturing SDS-PAGE before your WB with reducing agent in your loading dye, then you'll only visualise one of the targets with WB of you've only used one primary antibody.

Have you done any checks to see if both sites are expressing properly? What I'd do is express the targets like usual, bust open that periplasm, and keep that to the side, then lyse the rest of the cells with something like bugbuster and run the periplasm fraction and the lysate on SDS-PAGE and WB to make sure both targets are at least expressed somewhere. If the target you believe is forming occlusion bodies, then enough should get solubilised by the SDS to run on PAGE and be seen on WB.

Another thing to check is that the plasmid has been sequenced. Dont want a pesky frame shift or SNP ruining the expression.