Players are not always allowed to know the details of a check.
In particular, if it’s unreasonable for the PC to know how well they did on a check, the GM makes the roll and adds the PC’s modifier without exposing the actual roll value. Also, if a player wouldn’t know if they’re making a check, the check is made based on the PC’s modifier without telling the PC that a check was made.
The final information about the PC’s modifier is the version of the PC’s character sheet. If it isn’t updated, you may not be getting the results you expect.
Since we’re new to the Pathfinder rule-set, to encourage better understanding of the subtleties of the rules challenges will be rewarded. When the GM says the rules work a specific way, for that check they do. If a player disagrees, the rule is looked up. If the GM was wrong, that player gets a +2 on the next check using that rule. If the GM was right, the player gets a -1 to the next check using that rule. If the rule doesn’t directly apply to a check, the bonus/penalty is applied to the next role in general.
To encourage proactive behaviors to reduce the amount of effort the GM has to make to keep the game running, the GM may reward players with “GM Coins”. These coins may be redeemed at any time to affect an undesired outcome. For example: 1 coin can be used as a +1 to a roll. Players may suggest usages for the coins but the GM gets final say as to how and when the coins may be used.