There's two possible reasons when you get an alert with the message "Could not send message! Rate limit exceeded. We will try again automatically":
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Other apps (like another help desk app) are connected to your Gmail and Google is throttling your account. You can check for other apps on your account in this link: https://support.google.com/accounts/answer/13533235?hl=en
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The message you are replying to has been merged: this is a know issue and should soon be fixed!
If you're still seeing the alert and none of above are true, reach out to karri@commslayer.com and we'll help.