Well, it turns out that the bug is related to the way we sort the GAC and "referenced" assemblies together when displaying the popup list. The problem comes around if any "referenced" assembly is later alphabetically than the last entry in the GAC. In this case the assembly started with Z and the last assembly in my GAC starts with V.
So the workaround is
a. Rename the assembly
b. Sign the "referenced" assembly and put it into the GAC
Of course, if you don't have access to the code, you can create a do-nothing assembly called ZZZZZ or some such and put it into the GAC.
No, it's not pretty, but it should do the trick.