Hmmm...
2005, Indy at New England (regular season)
2004, Indy at New England (regular season and again for playoffs)
2003, Indy at New England (playoffs)
2002, no game
2001, Indy at New England (regular season)
2000, Indy at New England (regular season)
You're right... that's odd. In 2002 and 2003 they didn't play each other during the regular season and they've not scheduled a regular season game at Indy in the past six seasons.