A number of analysts have recently upped their third quarter earnings estimates for the banks based on QE3. In mid-September, Ben Bernanke announced that the Federal Reserve will buy $40 billion worth of mortgage bonds a month until the economy recovers. Mortgage spreads, the amount banks make on home loans, have widened 0.16% since QE3 was announced, and are now at 1.6%, or roughly three times as large as they have been on average for the past decade.

But some analysts may be getting carried away with their QE3 lovin’. When Bernanke announced the bond buying program there were only 12 working days left in the quarter. Yet, Richard Staite, an analyst at Atlantic Equities, estimates that QE3 will goose Wells Fargo’s (WFC) bottom line by $105 million in the third quarter alone, or nearly $9 million per QE3 working day.

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David Konrad, an analyst at Keefe Bruyette and Woods, recently upgraded his rating of Citigroup (C) to an outperform. His No. 1 reason: QE3. JPMorgan’s Vivek Juneja says he believes QE3 will boost demand for mortgages in the fourth quarter.

There has been some debate about whether the Fed’s bond buying programs will end up being a boon or a bust for the banks. While QE3 has boosted the banks’ mortgage business, overall the Fed’s efforts to keep interest rates low could hurt elsewhere. Mortgages are often sold off to investors or to Fannie Mae or Freddie Mac. As a result, banks are able to book an immediate profit. But in many other areas, banks often hold onto the loans they make. Lower interest rates mean they will make less money on every loan, perhaps for years. The longer interest rate remain low, the more high interest rate loans disappear. Juneja says he expects long-term net interest margins, which measures the profits banks make on all their loans, not just mortgages, to decline more than expected because of QE3.

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So the answer has to do with short-term versus long-term. In the short-term, the boost banks are getting from QE3 in their mortgage businesses is greater than the drag on profits in other lending businesses. The question is when will that flip.

The answer could be pretty quick. Atlantic Equities’ Staite, for instance, estimates Wells Fargo’s Bernanke boost is likely to dissipate to just $150 million for the entire fourth quarter, which translates into $1.6 million per working day. Still positive, but dropping quickly.