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There was a bug introduced in one of the recent versions that has already been squashed. If you have any timer pistons you either need to let them run wrong and then they will schedule correctly after that. Or you can pause/resume and piston with a timer and it will force it to reschedule.
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The clear button is doing exactly what it was intended to do. Just get them out of the way for now. As for the memory %, each piston has 100,000 bytes. This includes all the code, undo/redo actions, logs. cache of changes etc. Far less of a problem than people make it out to be if it gets high. If you want to clear up some actual space then fire up the ST app and in the webcore settings you will see
Clean up and rebuild data cache.
All future issues should be posted in a non deprecated thread. The latest is the Beta Milestone 2 thread.