We reported these issues in early 2012 to the developer.

Cooldowns fail to track appropriately on cooldown bar when:
1. a skill is placed on the shortcut tray more than once
2. skills are placed on shortcut trays 2 - 10
3. skills are placed on the extra shortcut tray

BHS closed the bug without a fix. At this time we are not aware of any future fix for this issue.