We changed a default last week (that I just changed back now, since we have been getting a ton of user issues over) to the way exposure is applied. In advanced options there are 2 ways to apply exposure, 'Each' and 'Group' We changed the default from Group to Each, which is now back to Group.

Here is a brief explanation of how each one works:

Group: if you set player A to a 40% exposure, and ask for 100 lineups, he can be used up to 40 times. Once he is used 40 times he is removed from future lineups. He could be used in the first 40, last 40 or anywhere in between. If however you ask for 100 lineups, but only 50 can be produced, Player A could be used in 40 of 50 lineups resulting in an 80% usage rate.

Each: if you set player A to 40% exposure it could use him in lineup 1, if he is used in lineup 1, he cannot be used for lineup 2, as that would make his exposure 50% (1 of 2 lineups). This way is more exact, meaning if you set a limit to 40%, that player will not be used over 40% no mater how many lineups are actually produced, which is why it halts and stops producing lineups when it would have to break this setting.

I think this is the issue you were having, I have changed the default back to group, but I will be adding today a setting that will remember whatever way you set this, so if you wish to use one way over the other you can.