Apparently, part of the hold up today has been last-minute bickering over changes to the controversial MTA payroll tax – a key element in getting the Senate Republicans to “yes” on the tax code overhaul deal.

Just to recap: Yesterday there were mixed messages on whether the partial MTA payroll tax elimination (depending on the size of your payroll as a business or nonprofit) and breaks for private schools would sunset in three years.

The governor’s office said “no,” the Senate wasn’t sure, the Catholic Conference said “yes” and then amended that statement. This morning, the Senate GOP said the deal would sunset – just like the tax code changes – in three years.

But that had changed by this afternoon, according to Majority Leader Dean Skelos.

Now we’re learning of a new wrinkle: Apparently, the public schools got very upset after learning that the private schools would be exempt from paying the tax under the new agreement.

Under the 2009 MTA bailout deal, the public schools have been paying the tax and then going to the state to seek a reimbursement. This is not only cumbersome, but temporarily causes a cash flow problem for the already cash-strapped school districts.

So, a new change: Now both the public AND private schools are exempt from the MTA payroll tax, which adds an additional $70 million a year to the cost of this agreement.

Actually, this year it’s $140 million because the schools, which operate on a different fiscal year than the state, have yet to receive their latest reimbursement. That bumps the whole cost up to $390 million in the short term and $320 million every year after that – remember, there’s no sunset anymore.