Will first say I had a late start on the game even though I bought it at launch for I needed to upgrade my GPU after a power surge from a lightning strike nuked my last one. I did not start the Family Matters quest till patch 1.08.3 was already out and downloaded.

Everything in the quest went fine till I examined the altar in the basement of the Baron's keep. After I examined it instead of having me go and talk to the baron, like what was originally in the quest prompt, it is telling me to re-examine his wife's room. Also, if I just try to talk to the baron he just says "Uh-huh" in this weird grunting sound reminiscent of a pig.

If anyone is able to help me with this I would be most appreciative.

Did you find Anna's talisman and Tamara's doll?

Yes, I Have the Talisman, the Incense, Tamara's Letter, and the Letter off the Altar all in my inventory. And, I did find the doll laying next to the bed.

After I found and inspected the altar and everything around it. It seems my quest for some reason backed up to the Search the room phase.

I hope I am not having to try and find an earlier save since I am one of those that always saves over last one. and periodically deletes old autosaves.

One more thing . Did you search Ciris room, found a toy and talked to Gretka? Maybe this will help. I understand that you red the letters. If you've done this I have no idea how to help.
I did stop deleting old saves for such rison. Better have buckup than start from beginning.

yeah,, I went ahead and explored Ciri's room and talked to the little munchkin across from it.

Only option I have would be to restart the game at this point which is going to suck,, character is already lvl 20 with full relic and witcher gear. I have been doing a lot of exploring, side, secondary and treasure quest. I think my propensity to explore has messed up another quest, the Phantom traders route one where you have to kill a royal wyvern, the royal wyvern will not spawn.

Though on a side note with the "Game+" DLC I can take my saved file and load it into a new game.

Ha! :) I've got similar problem with this quest. At first time, it didn't show up. Second time ( this is going to be interesting ), during fight wywern got under the ground !!! And to the end of the game was there slowly moving towards Benek, windmill and even now when I download old save ( the one after I finished the game ) still is over there and I can't finish this quest. I am planing to use NoClip cheat to see if this wyvern is really underground.

Yep :) I've just checked and I found it. It is just like I said. Look at screenshot :) Actually I solved this mystery thanks to our conversation :) Thanks :)
Anyway good luck and have a fun.

Yeah, sucks having to curb my explorer gene. Does not matter what game I play I will log hours of just running across each zone. In both Skyrim, Elder Scrolls Online, Dragon Age Inquisition, Oblivion, Morrowind, Baldur's Gate 1&2, my characters' legs would have looked like horses' legs if running actually changed the characters' appearance.

I do exactly the same. I love exploring. Before I move my story forward I do explore everything around and do all side quests. But because I am bored now after finish game 4th time I am using cheats to get to points I want to be and move as fast as possible.
Good luck on the path :)