Absolutely nothing. This is a problem with timers that has been reported. The fact that the problem still exists (I first noticed it in mIRC 6.0 which was the current version when I started working with timers) indicates that Khaled hasn't been able to find a workable solution to this problem (yet).
Please note that while the timer does keep ticking down, even after the pause command has been issued, the instructions to be executed when the timer expires, won't be executed until the timer has been resumed (/timer -r).