I had the same problem just the other day. I have a question for you. Does your water tank have a power vent blower? If it does, you will need to replace it even if it seems like it is working.
You will also have to clean the filter located at the bottom of the water tank. You will need to open up the sight glass door located in the front of the tank near the bottom of the water tank. But before you do this, please make sure that you shut off the supply gas valve to your hot water tank. You will need to remove the burner unit from the water tank by removing the four screws that hold the sight glass door in place.
Please note that you will also need to disconnect the little pipes that connect to the control valve where you adjust the water temperature. At this point you can now pull out the burner unit that holds the thermocouple and burner unit.
Please note that you will now see a metal screen filter that is not removable. It may look dirty or not, but you will still need to blow it out with a compressor unit that is set for 90 to 100 psi. Any dust or dog or cat hair will become dislodged and will be blown out.
After cleaning out the filter, you will then reinstall the burner unit with the thermocouple back into the bottom of the hot water tank. You will need to slip the burner unit in a slot that is located on the metal filter before you can install the sight glass door.
When installing the sight glass door, make sure that you install the gasket that goes around the sight glass door and then replace the four screws and re-hook up the small gas pipes that go to the bottom of the control gas valve and tighten the two nuts that hold the gas line tubes with a wrench. Next you can turn on the gas valve and start your system. You should use a soapy solution and check for gas leaks.
Please let me know if this worked out. The burner should run normal. By the way, what is the name of your hot water tank?
I hope this is helpful to you. If you have any further questions, I would be happy to answer them.