If you are running a metronome in MainStage, there's a couple important concepts to grasp about MainStage, the metronome and MainStage's beat clock that can help:
The green Play button represents MainStage's beat clock. When it's green it's running. When it's not it's off.
Anytime the beat clock is turned On, MainStage initiates a midi reset (unfortunately). This is why Tonic shuts off, sustained notes cut off, etc.
One solution is to just leave the play button On all the time (thus leaving MainStage's beat clock always running as well).
The wrinkle is that MainStage's metronome is forever linked to that beat clock, whether it is "On" or not. The metronome button in the top right corner doesn't actually start or stop the metronome, it just mutes/unmutes it. So, you have to get used to having to pick out the downbeat when you use it.
You can disable the downbeat at the concert level in the "Metronome" tab of the concert inspector if you want to.
If you prefer you can load an .AIF click loop file into an instance of Playback running at the concert level with the Sync mode set to "Bar" and Flex turned on to allow for tempo manipulation. This would allow you to leave MainStage's clock running at all times, and then map a button to "Play/Stop" within that instance of Playback- Playback would wait until the next bar indicator to come in, so you would not have your downbeat problems.
Check out this video for more: