I just want to get some clarity on this, please: "CA income consist of Commissions earned as an agent."

The Employee(s) of the corporation are Agents and get paid through payroll. The S Corp is an Agency, then? And also has Rental income? It's unusual for an S Corp to hold real property, and especially as rentals.

For most states most of the time you have to apportion income, not allocate it.

Apportionment uses income from each state, and sometimes property and payroll.

of course, the Shareholder is a real estate agent who earned commissions in CA and had it paid under the GA S-corporation. 

I agree, I wouldn't have had it set up like that either, but it was established as such prior to moving to CA.