Because you are disabling the mapped key (or at least the step of it) that you are currently running.
The second and third actions, for which you have "Modify DPS Rotation in Combat Hotkeys Key Map", should really be dealing with Virtual Combat -> DPS Rotation. This particular disable is the cast time it takes for this spell and you do not want to send another command to this character that will prevent them from casting the spell.
We don't touch the combat hotkeys, because we don't need to. We do as much of this actions in the middle of the chain, and not on the ends of it. The reasoning for thi will come later when you might end up with multiple steps or actions in the Combat Hotkeys. We disable the Virtual Combat because it really does nothing, except get replaced by the character specific Key Map, and if we disable the top of that chain (for a period of time), there is nothing to replace...... so we get the result without changing the state of all the important stuff. (NB. this one is the lessor of the issues, but it is a setup you should try and follow).
The forth and fifth actions should be disabling the step (6) in 110: MAG-Cubzytu -> DPS Rotation, not the actual mapped key you are running. You are running this mapped key, and then you want to disable it WHILE IT IS RUNNING. It will cause all sorts of things to not work as expected.
Anyway, heres a picture of it setup correctly.
- eqTimers.png (44.76 KiB) Viewed 13219 times
p.s. Some of your other Skills are also doing the same thing.......... and a couple aren't.