I'm really not sure what's happened but now all but one of my leagues sim on the same day, I have 12 teams.
The problem I have recently find is that I keep getting outbid on FAs. If you are only going after one player, thats fine you can go all out for that one player and offer stupid money, but if there are a handful that you could realistically go after, then you have to be tactical, and you just can't now.

First off you have NO idea how much anyone is offering other than what is displayed on the player card, (this needs updating regularly). Coaches you have no idea at all.
Might I suggest that if we are to have a level playing field for signing FAs and Coaches that there is a cut-off point of say 12 hours to get your bid in?

The bids are always blind bids and are not revealed until the stage runs if the player decides to wait. Even if a team withdraws an offer, it still shows whatever they offered as of the previous stage. When you view the pending contracts between stages does not matter.

Coaches are always blind bids and always sign the best offer on the table at any stage.

Maybe players should also be blind bids like coaches then? I don't understand why some of the players are revealed and not coaches bids?
I can put a bid in right before the sim, say that's 4am my local time, someone on the west coast has the advantage, and of course the other way around as well.

Coach bidding is just weird. I recently offered a QB coach an OC job and he rejected it and stayed as a QB coach, despite offering more money over a longer contract and (not that this factors in) a winning team. As far as I know I was the only bidder.

They are blind bids but at each stage the last stage's bids are revealed so that you have somewhat of an opportunity to compete with other teams. But whether you look at the bids 5 minutes after the free agency sim runs or 5 minutes before the next free agency sim runs, what you see never changes - even though other teams may have changed their offers.

So just to clarify, If I see a player with a top bid of say $20k over 4 yrs and 5 mins before the sim runs put a bid in of $25 over 4 years, it won't get submitted? If thats the case how long do we have before a bid can't be submitted?

Sorry misread what you previously said there.
So teams can put in new bids prior to one they may have put in, but it won't show up, I get that, but how many times does this update?
If they are not showing, what is the point in showing any of them?

Your bids are revealed to you, of course, in your pending contracts view. On the player card (an in the 'top bid' column) were the bids as of the last stage that was run. The point is that you have no more information 5 minutes after the previous free agency sim runs than you have 5 minutes before the next free agency sim runs.

So in your case, if you see a top bid of $20k over 4 years and you put a bid of $25k 5 minutes before the sim runs, that offer will indeed be submitted. But you don't know whether the team with that $20k bid still has that same offer on the table, or changed it to $30k, or withdrew it altogether. All you know is that, as of the last free agency stage, that team offered $20k over 4 years, so it's a bit of a measure of what you might have to offer to stay in the game for that player, and it's designed so that you have no competitive advantage if you wait until right before the sim runs to counter the existing offers.

The point of showing is to help drive up the competition and salaries for those players.

But if the most recent bids are NOT showing, then this is moot. Unless it automatically updates every time a bid is put in.

During the free agency stages the player in all likelihood will not accept an offer in the first week.

During the season, yes, it is moot - and you won't see competing offers except during the free agency stages.