At our house, antenna placement is very important...and we live less than 10 miles from television station broadcast towers.
It sounds like you're doing everything correctly with the converter box. You're receiving some of the channels wich means that the converter box is connected to the television, and you've gone a step further by resetting the "auto program" option on the box to allow it to find missing channels.
Our DTV Reception Problem
We had a powered antenna (Terk) that would pick up half of the available digital stations if it sat on top of the TV cabinet facing the couch; if we turned it on its side, we would receive the other half of the missing dtv stations. This was hardly an acceptable solution, although I did get a little bit of exercise for a few weeks having to get up and adjust the antenna every time I changed the channel.
What We Did to Fix it
I decided to upgrade to the Antennas Direct DB2 antenna after reading some good reviews on Amazon and a few other sites. I was a little concerned about the size of it (Dimensions 12" H x 19" W x 4" Deep) and to be completely honest, it's not exactly pleasing to the eye.
After installation, not only did the antenna bring in the missing channels, it's placed behind the TV cabinet...completely out of site from anyone in the house but the dogs.
You may want to expirment with another antenna. I purchased mine from a store that had a good return policy just in case the results were not what I was expecting. The odd thing about antennas is that each one has it's own advantage depending on many different factors. I'm sure there are many applications where the Terk (UHF/VHF) will actually perform better than the DB2...this just wasn't the case at our house.