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1. Since all your high-frequency data appears to fall victim to decreased frequency when bagging, can you try bagging to another disk? It seems like very strange behavior to me, and unrelated to r_l.
2. Can you run top or htop to see if something is consuming a lot of CPU? Also, let me know how much CPU r_l is using.
3. I noticed in your config file that the debug flag and corresponding path are specified, although I recognize that debug is set to false. Just an FYI: if you're running live and turn on debug mode, it's going to eat a lot of CPU and slow down the filter.