Have you adjusted for spread and/or difference in team quality? I'd ask this because bowl games and CCG's (which make up majority of neutral site games) generally tend to be pretty even matchups, while home/away games (both in and out of league) have a great many mismatches. Assuming that your analysis was basically "what is the record of the higher rated team", I'd assume this would then explain it.
That's probably easy to check; you could bucket road/neutral/home games into buckets based on how different your power ratings are for the two teams (near tossups, mild mismatches, major mismatches, expected blowouts, etc.), and then see what the varying win %'s are inside of each bucket.
I did something a while ago that wasn't QUITE like that, but was along a similar vein, basically using league records as a proxy for team quality, bucketing games by how different their final league records were, then looking at home/road splits (neutral site league games are rare enough to not be worth adding to that analysis) for intra-league matchups only
cfn.scout.com/2/1059791.htmlI also did a follow-up on that, looking specifically at the impact of distance on home-field advantage, basically concluding that HFA is in fact dependent at least to some degree on distance.
http://cfn.scout.com/2/1063535.html