So I just finished watching the second season and for the life of me, I simply do not ever recall seeing the final three episodes for this season: "Double Parked", "alice's september song" and "Tell it like it is". Would anyone happen to know if these three episodes are somehow left out of the syndication packages for the show because I swear, I never saw those three episodes of the series and I thought I had seen all 117 episodes.

Nope--there were never any "left out" episodes. You most likely missed seeing them in the rotation.