I have had this issue in the past, and didn't take advantage of Compiz as a result.

Problem: With desktop effects enabled on a dual monitor system, window menus are slow to open (1 or 2 second delay). You may notice that this is only true on your primary monitor, and that they are full speed on your second monitor.

Here is the answer, found at the Ubuntu forums. A bash script that launches Compiz separately for each monitor.
Ubuntu Forums - View Single Post - Dual Monitor Compiz-Fusion Slow Menus and Window Resize