It seems the timer is moving to fast on games although I haven't paid much attention to it until today. Also, I had some games time out that I thought I had a lot more time on. Then, when making a move today on a 2 day per turn game, right after I made my move it said my opponent has 47 hours left. What happened to the 48th hour?

It just seems off but I'm won't know for sure until I manually record a time and match it up to a real clock to see if chess.com's clock is running too fast.

Nothing is wrong, it's just a way how chess.com displays the remaining time.

I think it's perception- sometimes I'll check and think to myself, surely more than a day has gone by on that game...? other times it goes by quickly.

As for the 47 hours thing, it's like charging $2.99. It's really $3 but the part on the end gets ignored so it looks like its only 2 bucks.

Explain this please. I made some moves in other games earlier today and they still say 2 days left for my opponents to move. In the same game that I noticed the 47 hour result I just made another move and once again this game says 47 hourse.

Why the difference?

The time displayed on the game page is rounded down to the next full hour.  If someone is playing a two day game, the instant their opponent moves they have 48 hours, but one minute later they have 47 hours and 59 minutes.  The display will say 47 hours.  If you want to see exactly how much time is left, including the minutes, click on the "details" tab to the right of the game board, and there it will say 47 hours and 59 minutes.