but every time I change the instance variables to start a new set of objects with different a timer setup, the previous set of timers stops.
You mean you create a few new instances, start timers for them, but this stops the running timers on previously created instances?
This should not happen. You are probably not picking the right objects in your loop. Can you post a screenshot of your events, or project file?
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Also, this event will not work:
OBJECT On timer "Name"&ObjectInstanceVariableName Actions
"On timer" events need to be hardcoded. Or you need to check them in a "For each" loop on every tick.