It's just that the stress of multiball is causing the game to reset now. It will get worse and more frequent. Unfortunately there isn't just isn't one thing that causes this but many. The pinwiki above will guide you through a process to help identify and fix the issue.
This is a very common issue that deals with the +5V on the power driver board and on the CPU board. When this drops down below a certain threshold (about 4.8V) the watchdog circuit will reset the game. Now finding and fixing the issue may take some time.
The easiest thing to try is to reseat connections at J101, J102 and J114 on the power driver board and the Z-connector between J114 and the CPU. If that seems to help you haven't fixed the problem you've just identified it. You'll need to replace the headers and connectors. If the above doesn't work, you'll need to start digging...