I have the Windows Taskbar set to auto-hide and keep on top of other windows when it does appear.
A few days ago (I installed Process Tamer on June 26) the taskbar started appearing at random intervals (every few seconds/few minutes). It would sieze focus and the usual method (click elsewhere on the screen) would not cause the taskbar to hide. After a while, it would hide itself - until it popped itself back up again. Very inconvenient and annoying.
I didn't immediately make the connection between Process Tamer and this new taskbar behaviour. Then I noticed PT was set to Show System Tray Balloon Messages on all 3 events listed on the Configuration page.
I turned off Show Messages for all events yesterday, and the taskbar has reverted to its normal behaviour since then. So I figure that PT's Show Messages was causing the odd taskbar behaviour.
Note that balloon messages for tray items are currently appearing behind the taskbar - a known Windows bug - and I wonder if this is a necessary condition for PT messages to cause the taskbar misbehaviour?
I don't see any other reports about this oddity in the forums, thought you might like to know about it.