Quote from stevegee58:
If you use the 2 factor authentication (either the security code card or the fob) I don't believe either of those programs can relogin without your manual intervention.
Quote from brocklanders:
No, you can, despite either type of token (card or fob) you can still have IBController login for you. There have been issues in the past with it re-challenging you but I believe those to be isolated to certain versions of TWS and I have not personally found that to be an issue.