Are you using the iassembly factory file to create the drawing views (you should be)?
Do not use the generated member assembly file.
Use the factory iam file (the main iassembly file) and when placing the base view go to the model state tab and pick the iassembly member from the list there.
Then the parts list should include the proper components from the base view.
You can also edit the parts list and hit the member selection button if you need to include/exclude other members from the parts list.
IMO you should NEVER use the member files to do anything in Inventor.. Everything should be done using the factory file and then selecting the proper member from that.
Forget you ever saw where the members are saved and never open them explicitly. Use the factor iam file always.