Water Heaters - Pilot hard to lite

Brand new hot water heater...The water supply line had a bad connection and started to leak. The water from the leak settled in the pan the heater sits in. Not sure how long the leak had been happening. Called tech support and they said to drain the water from the pan and let dry out. done and done..however now the pilot is hard to light and when it does ignite and I turn up the temp, it catches but then it gets snuffed out along with the pilot. From there the pilot won't ignite until I wait at least 5 hours, but then the same problem occurs? Could the water move some sediment around and cause blockage? venting is not the issue, checked it and it was clear.

Sounds like the arrestor plate in the bottom of the heater under the burner still has water blocking the openings. The blockage is causing the burner to be starved for combustion air. Me thinks

I could be way off here but,

Is it possible you have the wrong gas type water heater?

Also, some of the newest water heaters are coming through with all kinds of sensors that could cause the problem.