I had this same problem too. One other problem that this situation may cause is a large increase in the cpu utilization and time that it takes to recalculate the pingtree topology. One of my network guys inadvertently remodeled one of our edge routes to an internal 10.x.x.x network. I ended up having over 6600 networks with multiple subnet masks. Every time a change was made to a device, zenhub would hog 100% of the cpu for over 20 minutes. Once I went through a lot of the steps you suggested and got the total number of networks down to under 100, my network map worked and the pingtree calculation dropped down an acceptable level.
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