Full Disclosure: I am playing the game using Wine in Linux, so this might be Wine-specific.

I came across a bug in the game, where the countdown timer (which is used in the first stealth mission) is missing from the screen when the "scaled" option is set to "1.4x". I suspect what is happening is that the timer's placement is not being adjusted with the scale, and is positioned below the bottom of the screen.

If you are playing a level where the timer is supposed to show up, but isn't, try changing the scaling to "1.0" for that level, and you should have the timer visible again.

Hi;
this is not Wine-specific, I ran into the same problem in the Sneaking mission while playing on Windows 10 with resolution set to 1920x1080 and scaling to 1.4.

I didn't even know there was supposed to be a timer until I started to fail the mission by randomly de-cloaking with no apparent reason.