This is a new issue... I had the same situation (2 1099Rs from same broker, different SSNs, same amount) last year and electronically filed, without incident.
I am reluctant to add the penny so am just sucking it up and paper filling this year (for the first time in as long as I can remember).
Since there is a document ID on the 1099-R (like on a W2), if that went into Turbo Tax, they could tell them apart. Seems like it is a TTax issue in the way the data is being organized and transmitted to the IRS.
