I just deployed a new update to the HTML5 version, with several bug fixes:
Timers have been completely rewritten to run as a part of the main game loop, so they will always stay synchronized. Previously, timers ran outside of the main game, so two timers both set to identical delays and started at the same time would not always trigger on the same frame - now they will. This means you can now do things like connect two timers to an AND gate and have it work reliably. As a side-effect of this change, timers will now pause when the game is paused.