I haven't had issues with back-to-back trips; granted they were flown with different airlines/alliances.
Roundtrip 1 on UA: Depart IND-MHT Sunday week 1, return MHT-IND Thursday week 2
Roundtrip 2 on NW: Depart MHT-BNA Thurdsay week 1, return BNA-MHT Sunday week 2
As long as you use different airlines, you should be fine.