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Remedies for some positioning issues with SPRY Horizontal Menu (tested version 1.6.1)

The drop-down submenus appear underneath other <div> tags.

The SPRY Menu may not be be placed within a <div> tag which is positioned 'relative'. Try a 'static' positioning for the DIV which contains the menu. DIV blocks that follow after the SPRY menu DIV in your page may have: position: relative. That doesn't hurt.

The SPRY drop-down submenus appear underneath FLASH objects.

Since FLASH will appear by default as the top-most layer (z-index) possible you should try following work-around: Set the Flash movie window mode to transparent which is done in the OBJECT or EMBED tags of the movie. If you are using any scripting classes which place the FLASH onto your page then you have to check the documentation.
Here's the parameter:

The SPRY drop-down submenus appear underneath SILVERLIGHT (v2) objects.

Add following parameters that are the equivalent to the above mentioned FLASH parameter. Add them to the Silverlight tag which you use to place the movie onto the page.

These techniques helped in my case.