The timer doesn't change anything as mentioned, it just makes an activity record so you can see the stats for that time (if you expand the record). You can actually edit the start/stop times if it was turned off or even make an activity record if you didn't use the timer.
If you log activity to fitbit, Spark doesn't pull those calories over. That is just how Spark has it set up, I know two other nutrition tracking apps that link to fitbit that do pull over the calories manually logged to fitbit. I am not sure why Spark decided to do it this way, but I kind of like it because Spark pulls too many calories over from fitbit anyway.
I agree email customer service, what you are describing doesn't sound right. And why is your timer turing itself off? (It can happen if you accidentally push against the button through your clothes, but otherwise ti should stay on until you stop it). Maybe something is wrong with your device?
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