My folks have Comcast in Chicago and their channels are as messed up as yours. You basically have to memorize where the different channels are located in order to flip around.
Here in Mississippi, however, the channels are fairly well organized. All of our local stations, including PBS and WGN, are included in the first 13 stations. All but one keep the actual channel number that they would have on a regular TV. All of the ESPN stations are contiguous. All of the do-it-yourself stations are together as are the shopping channels. The free movie stations like TMC and AMC are close as are all of the Encore stations.
I have no idea why some local comcast affiliates have the channels so poorly organized.