How come sometimes when I am playing and have my auto import and HUD on that my results dont transfer to PT?, 98% they do but there have been a few sessions when I will have a sizeable profit but PT says I am in the red??? I contacted FT support and manually imported my hands from that specific day in case for some reason the PT software didnt import it...I refreshed PT and it still says I am in the red when I know this is wrong, I hate not having the right info like my profits, graphs etc because I am relying on it for my personal knowledge but more importantly tax reasons.

Please attach the hands in question to a support ticket and we'll investigate what is going on here for you.

Im not sure where the hand histories are...is there ever a reason that hands will be auto imported to PT with all your correct hands, opponents, stats etc but actual results not correctly uploading? it has happened to me a few times but after a day or so the right data will somehow finally be retrieved...but this time I still have the incorrect info and it has been almost a week

By default hand history files are moved to the PokerTracker 3\Processed folder after they have been imported, so you should be able to find them there.

Have you clicked Refresh after the session? The reports will not update until you refresh so you need to do that to see newly imported hands. If the right data is showing up eventually then it has been imported.
Another possiblilty is that you have a filter enabled - click Clear.