well ... lemme explain
you are playing in hotkey / semi-auto mode
both modes are working this way:
- Cast single target rotation
- Use Cooldowns (Alter Time and so on)
WHEN the Hotkey for Cooldowns is pressed (by default it is ALT + Q)
- Use something total superb
WHEN the Hotkey for Special things is pressed (by default it is ALT + F)
difference between both modes
- Auto-Semi switches between Single and AOE mode without pressing a key
- Hotkey switches between Single and AOE mode by pressing the hotkey for AOE-Mode (by default it is ALT + E)
everything u enable by pressing a key, has to be disabled by pressing the key again, if u don't want it to be used anymore
AutoMode will do:
- Cast Single Target roation
WHEN needed
- Cast AOE rotation
WHEN needed
- Uses Cooldowns
WHEN needed
- can't do any superb special features (for mages: Time Warp not supported since it could be wrong)
so every issue u have atm, is related to yourself

Time Warp is casted on CD cause you enabled it by Pressing ALT + F, but u never disabled it by pressing ALT + F again
same for Alter Time, it is never casted because u never hit the Cooldowns key (ALT + Q)