RealGM

I really like nba.com's lineup tool because of the filtering and sorting, but I can't seem to find a way to filter to just starting line-ups. If the "Group Qnt" category had Starting Lineups instead of just 5 Man Lineups, it would be exactly what I'm looking for.

http://stats.nba.com/leagueLineups.html

I can tool with minutes and get a good idea, but if a team had a routine early sub in the rotation, then it throws everything off.

Not sure if this is exactly what you are looking for, but popcornmachine.net has a chart for every boxscore showing when each player was on/off the court. Not sure if it is in a format that is downloadable or usable in large quantities, but you can see exactly when DeAndre sits in the third quarter of each game, etc.