These "blank" parts in the time graph on intermediate hops come when the route changes and the router you're looking at is no longer participating in routing data to the final destination. During those periods, another router is collecting that data.

You can see the route changes in the left side of PingPlotter. We have a knowledge base article that discusses this a bit here:

http://www.nessoft.com/kb/65
also here:
http://www.nessoft.com/kb/30

Hopefully, that answers your question!