I am new here. I found this thread as a result of a search. I have exactly the same problem as the OP. The Taskbar 'flashes' very quickly into view. It is not regular and seems to happen more often at times. I believe it may be related to other tasks that may be coming alive in the background.
In any case, it is very annoying. My system is new and came with Vista installed so there is nothing 'left over' from a previous version. It is an Acer M5620. After I read through the posts, I realized that I may be able to identify when this started. Since this was my first experience with Vista, I had early on switched the Desktop Appearance to 'Windows Standard' just so it would have a familiar look and feel. Not long ago, I decided I was familiar enough and was willing to try the Vista appearance, so I switched to 'Windows Aero' and I believe that was when the flashing started.
Anyway, I just switched to 'Windows Vista Basic' appearance. That looks like it has either entirely corrected the problem or much reduced it. I will watch for a while and keep you posted. My next attempt will be to go back to 'Windows Standard'.