It’s not as if bank stocks don’t have enough problems what with the horrible mess that they’ve made out of their mortgage business: If you can’t foreclose on a house because your paper work was signed by employees who never even read it, you’re in deep, deep trouble.

But let’s not forget the problem that will remain after all the foreclosure headlines have gone away: Banks, U.S. banks at least, are having trouble showing much growth in their basic business.

That was the message in JPMorgan Chase’s (JPM) earnings report morning on October 13. Earnings per share came in better than expected, but revenue came up short.

And JPMorgan Chase is, many analysts say, the best managed of the big banks at the moment.

Before the open on October 13, JPMorgan Chase announced third quarter earnings of $1.01 a share. That’s 11 cents a share better than the consensus expectations among Wall Street analysts.

If you thought that would have set shares flying higher, you’d be wrong. Shares actually started the New York trading day down slightly.

The problem is that while earnings beat projections, revenue didn’t. Revenue dropped 15.4% from the third quarter of 2009 to $24.34 billion. That was less than the $24.64 in revenue expected by Wall Street.

The good news on earnings was a result of continued improvement in loan losses and delinquencies. For example in the company’s credit card business charge-offs and delinquencies improved enough so that the company was able to reduce loan loss reserves by $1.5 billion. That’s a big switch: from a past hit to earnings to a current addition to earnings.

The problem for revenue, though, was that some of the company’s key businesses didn’t show any growth at all this quarter. Revenue from JPMorgan Chase’s investment banking business, for example, fell to $5.4 billion, down from $7.5 billion in the third quarter of 2009 and $6.3 billion in the second quarter of 2010. That drop in revenue was big enough to take investment banking net income down 33% from the third quarter of 2009 in spite of the release of $142 million in loan loss reserves back into earnings. Going into earnings season analysts had worried that low trading volume in the quarter would hurt investment banking revenue at JPMorgan Chase and other big investment banks.

Fixed-income revenue, a big concern among analysts before the earnings report, dropped to $3.1 billion from $5 billion in the third quarter of 2009 and $3.6 billion in the second quarter of 2010.

And in contrast to the significant improvement in credit card losses, the bank reported continued losses and charge-offs in its mortgage and home equity businesses. Home equity net charge offs came to $730 million in the quarter. That was a drop from $1.1 billion in the third quarter of 2009 and the net charge off rate fell to 3.1% from 4.25%, but total charge offs for mortgages and home equity loans came to $1.2 billion. The bank also took a $1.5 billion loss on bad loans it had to repurchase from investors.

In other words JPMorgan Chase isn’t out of the mortgage woods yet. “We expect mortgage credit losses to remain at these high levels for the next several quarters,” said CEO Jamie Dimon. “If economic conditions worsen, mortgage credit losses could trend higher.”

All in all, I’d say these results are okay news for JPMorgan Chase—no big negative surprises but questions remain about when investors will see real growth in the bank’s businesses. But they sure don’t remove the doubts hanging over the big trading banks such as Goldman Sachs (GS) and over smaller banks that had bigger loan loss problems than JPMorgan Chase during the last few quarters.

Full disclosure: I don’t own shares of any stock mentioned in this post in my personal portfolio. JPMorgan Chase is a member of my Jubak’s Picks portfolio.