As a plumber I have had the opportunity to install many types of heating systems. There is realy no simple answer to the shrinkage issue.
Having installed many systems without humidifiers in New England.I can honestly say it is going to be tough pointing a finger. I have seen shrinkage in millwork in houses with humidifiers and no shrinkage in houses without. In one of the cases it was extremaly wet when the house was built and it wintered with the heat very low. the following winter the house crack upart at the seams, when the heat was turned up.
When I do radiant heat I recomend acclimate wood flooring and baseboard in the house for a week to ten days and a moisture level between 6 and 8 percent before installing wood flooring. This prevents the floor from shrinking. Which brings us back to your problem. What was the moisture level of the millwork in your house when installed. What was the moisture level in the house framing. Not knowing this is tough part. This is why its hard to point a finger. You might have better luck dealing with your general contractor. The contractor has to warranty the house for a year.