That's not a problem, it's by design.
Due to timeout protection, when the player gets too low on time from any of their games, they automatically go on vacation on all games (excluding no vacation tourneys). If they then get on the site, and come off vacaction quickly, they get docked 24 hours of vacation time and some time gets added to their games.
If they don't come on until 24 hours after the games get paused, that doesn't happen and I believe the time added is 24 hours minus the amount of time already spent paused.
I have a problem with this game: http://www.chess.com/echess/game?id=94986576
My rival doesn't play any move but his time comes back to "24 hours" all the time!
Catch a glimpse?