If it is only happening in multiball, then it sounds like all of your trough switches needs to be checked. The game think it hasn't given you the proper number of balls for the multiball, as one of the trough switches is likely remaining closed.

take all the balls out of the machine and enter switch tests. I am guessing one of your trough switches will still be indicating a ball is in the trough. If that doesn't find the bad switch for you, then take off the apron, take all the balls out, and enter switch test. Then just play with the trough switches. Including rolling a ball through the trough and seeing what the switches do.

It has to be a switch. If they are working in test mode then you need to see if there are situations where they are been triggered or not triggered when the opposite should be occurring. For the switch above the coil that kicks a ball into the shooter, mine appeared to work, but would sporadically, so in test it would work like every 5 time I pressed it. In addition, it was bent slightly so that ti was not getting fully depressed when a ball was present.

Essentially you are looking at 7-8 switches that could be having an issue. If it was my machine, i would personally shotgun the problem and just replace all the possibly bad switches. I know its overkill, but it is not like those switches are that expensive. Then you know they are all new and wired correctly (assuming you know what your doing).