You're probably right; it sent in your return with no payment; and you'll receive a bill from the IRS. I don't want to bad-mouth TT based on my own limited experience with it, but this kind of stuff is what I've come to expect from popular tax-prep software in general. You may want to hit the TT forums for advice -- or if nothing else, to vent about it.
You'll probably want to make a payment before you get the bill. You can do this at the IRS website so you don't have to mail a check, and you'll get an instant receipt.
If you get late-payment penalties, you can try to abate them by filing Form 843 and explaining what happened.
If a "for cause" abatement doesn't work, look into requesting a "first-time abatement", which is where the IRS removes the penalties just to be nice. I've used it successfully before.
But assuming you've filed on time, the late payment penalties are not too bad; I believe it's currently 0.5% of the amount due, for each month you're late. If that comes out to a few dollars, you probably just want to pay up, send a nasty letter to Intuit, and move on.