Edit NOT SOLVED!
the factories drawing mats randomly from storage on planets issues is just a visual glitch, if I delete or make a new link and hit submit mat counts in all storage get properly updated AND you can actually set priority in order of routing, so if you route mats from a launch pad then a storage it will always take mats from the launch pad first and then the storage, you can see in the pics that after I deleted an extra link that the values in the storage and the launch pads were correctly updated. so no worries about crushed jellies 
you can see in the first pic that the numbers are off in the storage but after deleting an extra link the levels are back to what they should be at.
