Microsoft really need to clean up the timeline shapes in Visio, they're kind of buggy (especially if you try and overlay things on top of them - the timeline intervals will always force themselves to the top)
I know some of you might say use a proper scheduling program but I use visio to make timelines that don't look poor which in turn a much easier to "sell" to the business (presentation is often 50% of the battle sadly)
Scheduling tool is typically the Gantt chart, but, that probably doesn't meet your visual pizazz factor.
The interval shapes do like to be on top, but, that can be altered. Place a shape you want on top, somewhere on the page. Then, either press the key combination <cntl> + <shift> + <F> or go to the menu bar > Shape > Order > Bring to front. This will elevate the shape to the front most position. Now it will be on top of any interval that you've already placed. ;) However, any newly placed interval will take precedence over these shapes. You'll just have to bring them or any new shape to the front. :P Moral of this story -- place all of the intervals 1st. ::)
HTH
Wapperdude