Definitely using the flash meter correctly, I've gone back to the manual and triple checked I'm not being stupid! If this issue is being caused by user error, it's somewhere else in the chain!
One way to test whether the problem is caused by the shutter is to set up in darkened room. Open the shutter on “B” or "T", fire the flash manually, then close the shutter and process the film. If the problem persists, then the shutter is not the problem. If the problem disappears, then the shutter is likely at fault.
I haven't used my flash meter very much at all yet, but I do recall in the manual that there are two modes for flash metering, one of which is cumulative, and is specifically designed for using multiple flash units.