Thanks Thomas. My company indicated that they are required by the IRS to use the same EIN as I explained before. They also indicated that tax software keying off the EIN does not recognize the name difference when a company acts as an "Agent for...". Thus, their recommendation is not to file electronically, but to submit by mail, with highlighting on the name difference and providing the rationale they gave me. (See previous post). They do this for more than one hundred employees each year since it is common for employees to transfer among the various business units.
The last time I transferred to a different business unit was about 5 years ago and TurboTax correctly handled the over payment (two W2s, same EIN, different names). Perhaps they can do it once again.
