What OS are you using? Natron on Linux has the reputation to be more stable.
Hint: if you rotopaint over the result of a compositing graph, then use the disk cache node to cache to disk everything above rotopaint. This make things a lot easier (just think about all the operations required to render just one pixel of your rotopaint output - every rotopaint stroke is actually one or two more nodes in the internal graph): http://natron.readthedocs.io/en/rb-2.3/plugins/fr.inria.built-in.DiskCache.html
In any case, clearing all caches should be preferred over manually changing parameters back and forth.