Can you share the Python script you're using to re-cook the network? Doing a shift-v on a TOP node is the same as calling the following, where top_node is the selected node:
top_node.dirtyTasks(False) # True/False indicates whether output files on dirtied items should be deleted top_node.executeGraph(True)
If you have a reference to the TOP Network itself, you can use network.displayNode() to get the TOP node in the network with the output flag.
I don't have Houdini in front me of now, but I can try to reproduce the problem next week. If you're able to send an example HDA that demonstrates the issue, that would be helpful.