We continued to see this issue sporadically for a long while, but I had a breakthrough last week when trying to add a new input.
When using ORDER by DESC to find the latests checkpoint value for a query that I was troubleshooting, I accidentally kept in that ordering when I accepted and created the input. Verifying the new input, I noticed a bunch of event duplication and an equal amount of data indexed each polling interval. It seems that if DESC is set in the SQL query for rising column inputs, the input will be treated similar to a batch input, so each time the polling interval is met it will increment the checkpoint value to the newest one and backfill until the maximum number of entries for each polling interval is met. Just a heads up, DESC is an easy way to find current events, but not good if you save if that way.
tldr
** always use ORDER BY ASC for rising column inputs **
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