Yes, you are correct. Technically, you don't have a bolted connection problem, you have a file naming problem. By having multiple files with the same name under the same project file, you are setting up a situation where Inventor is not sure which to use when it loads your assembly.
So far as I know, the naming is automatically incremented (Bolted Connection1, 2, 3, etc), but only within a particular assembly. Therefore, the first one you add to each assembly will automatically be named as Bolted Connection1 (unless you manually change the name).
