I don't think the beep is related to the card. I just removed the card from an ST12, bound it to a Q500, and flew a few minutes in hover about 10 ft. altitude. No beeps.
Is the beep sound a sharp "Beep", or more of a Buzz?
Did you notice any changes on-screen, such as loss of GPS, warning screens, any differences from normal indications?
Is the interval between beeps completely random, or does it seem to follow some pattern. Especially, does it seem to occur in coincidence with any control function?
I don't have much to offer. However, many odd behavior issues can be cleared by deleting the existing model, creating a new Model, and binding the ST-12 to the new model.
I would also check the "hardware monitor", and look for any responses that are jerky, uneven, slow to activate, slow to return, etc.