First of all, it would be worth creating a true 64 bit install with only the merge modules to verify that the modules install OK on your test system. If this works OK, you could try adding the 32 bit MSI as a nested installation - this may get around any issues with mixed installs.
Can I also check whether this package is intended to deploy two independent bits of software, one 64 bit and one 32 bit, as if not, I can see issues arising due to the 64 bit content being registered in the 64 bit part of the registry, where the 32 bit application has no access.