The first thing to check is that you're actually going against the same target. You probably are, but we've had numerous situations where we're helping someone solve a problem like this, just to find out that there was some difference in the targets being traced / pinged.
Next, have a look at the packet type. MultiPing only supports ICMP packets - so in PingPlotter, you want to pick "ICMP Using Windows DLL (default)" as the packet type. Also, make sure your "Timeout speed" in PingPlotter matches your "Ping Timeout" in MultiPing and that your trace interval is the same.
If these are all the same and you still see different results between the two, try switching PingPlotter to ping the final destination only (View -> Ignore first hops -> Ping Final Hop Only). If that doesn't show any difference, then the only thing left is to change the packet type in PingPlotter to match MultiPing. If you get through all the above and still can't see a difference, let us know and we'll tell you how to do that.
Let us know how this goes. If you still can't get things working the same, then email your ini files (PingPlotter.ini for PIngPlotter, MultiPing.ini for ... well ... MultiPing) and we'll see if we can see anything else that might make them work differently.