Thanks HVAC. I had already investigated the ECR website and noted the parts change for the pilot orifice and pilot light which is what I was going to tell Sears tomorrow. Plus I will be calling the TECHs at ECR to see if this is a common problem.
If the boiler is under warrenty since you just purchased it then you should have NO problem with them replacing the burners because that can possibly fix the problem. Now to be honest with you Sears service and install has never impressed me to start with but under these circumstances let them do the job under warrenty and see what happens. I am sure they already have checked the gas pressure regulator and made any adjustments necessary to eliminate that problem.
I have enclosed a install manual since you may not have one since you did not install the unit. It is handy to have for part numbers etc.
One thing that happened years ago and it would be a very remote possibility in your case is that the burner that is having the problem has the wrong orifice installed. This can happen at the factory or if the unit was changed over in the field from natural to propane gas. Just a thought on my part.
http://www.ecrinternational.com/secure/upload/document/1195.pdf
Below is a link for a problem with the pilot lite. It is possible you have the old style depending upon your serial number. If you are not having a problem with your pilot now you will in the future and I recommend you call Penco at the number provided to see if you need to replace yours. They will send you a new pilot for free and you can have it installed at the same time as the burners.
NOTE: the pilot problem has no bearing on your current problem. I just saw the repair TSD release and provided it here as a service to you to prevent possible future problems. Good luck geting it repaired and post back with the results.
http://www.ecrinternational.com/secure/upload/document/1514.pdf