Sorry my friend, I have no answer to that, except I can complain to the same tune.
Gaining time on the clock

Their auto-timeout protection is activating. When the clock reaches 90 or less, auto vacation is activated for premium members. This then removes 24 hours from your vacation time and in turn adds 24 hours onto the game clock, hence the time difference. One day is still lost from vacation time though - when the alert arrives to you, there is infact less than 90 minutes remaining on the clock, but the 24 hours vacation time added to it shows when you log in and remove vacation time.
This is to prevent "vacation" time being used to just manage an over-loaded games list.

Thank you jac1yn,
Your answer certainly agrees with my experience. One of my opponents was down to 85 minutes and came back with 24 hours. I am a premium member and appreciate the automatic vacation feature and the idea of charging 24 hours whenever it is used. But I feel it would be more fair to return from vacation with the same amount of game time as when you left. I would happily accept that condition being applied to me in my games.
I've had games where my opponent went on vacation with only a few minutes left then came back with a lot more time. Why is this?