I had the same problem, and I have a solution. I had a table with a select handler and links that I wanted to open up in new windows without triggering the select handler or altering the selection.
I was seeing the problem where the link was not receiving the click. This was because my table selection handler was updating the data in one of the columns in the table and redrawing the table so that it would reflect the change. The redraw of the table destroys all of the elements, so the link never receives the click. For testing purposes, I removed the redraw, and the link would be followed but I still had a problem where clicking on the link would change the selection in the table, which I did not want to happen.
So, here's my solution. It's ugly, but it works. I use the onmouseover event of the link to store the selection and remove the select handler. Then, the link will function properly, and I use the onmouseout event to restore the selection and add the select handler back onto the table.
David