Hello,
It seems that the timer settings in custom games permits the continuation of the timer countdown even when the game is paused. As a result, the game ends when this internal (hidden) limit is reached even though the displayed in-game timer shows remaining time. For instance, if the game is paused for five minutes in a custom game of 15 minutes, the game ends at about 10 minutes per the in-game timer. This has been tested through different patches for default 1v1 settings.
Thanks for looking into this