Hi Gabe,
Sounds like your MIB isn't "reloading" its commodity fast enough. If you only want a certain MIB to load only, then "0" (zero out) the half of it that Consumes and set Produces to max. As a rule, MIB's can be rather tricky to get right. If you are loading many cars, then both the Rate and Produces have to be set to max.
You might make a test and have your train load up and then have a second train come by and load up immediately after the first to see if the MIB can produce what you think it should.
FWIW, I never save a session mid-stream and only run trains by "AI" only. Hope this helps you some.