It was mentioned that the Boxey kid was dropped for a number of reasons. He originally was to be Boomer's "sidekick" and there was going be a family type dynamic with Tyrol and Sharon but then they decided that Sharon would be a Cylon at the end of the mini so he was just to be a "in the background" kind of kid but his scenes from the first season mostly got deleted. You can see them on the DVD set...they are ok but they just seem out of place in the context of where they decided to go.
More importantly, while they liked the actor, he by his very nature of growing up from being young looking in the mini series and season one changed as they went into season 2 and since the events from the mini and to present day season 2 only take place over the course of 9 months, and the actual actor as a kid aging nearly 3 years from the mini, they just couldn't justify how this kid they picked up suddenly grew and looked older faster than he should be.