1. Doubt the Transfer switch is bad. It is extremely rare for a transfer switch to only close 1 leg of power.
2. Your EMS senses the OUT OF PHASE 2 -120 legs of power. IF those 2 legs are on the same phase, the EMS assumes you have 30 amp service
3. VERIFY that you have double the line voltage between the 2- 120 legs at the 50 amp service pole(3 and 9 position). IF NOT, you do not have 50 amp service. But, "Cheated" 50 amp service. Cheated is a 50 amp breaker on the same phase supplying ONLY power on a 50 amp breaker and not a TOTAL of 100 amps which is true 50 amp service
4. EMS systems do not have to be "set" to 50 amp service. It is Automatic when connected to true 50 amp service. You cannot even change to 30 or 20 if on 50 amp service.
Do these tests and post. Doug