I found the solution digging into the forums. The solution was given in the following link:
http://www.telerik.com/community/forums/aspnet-ajax/docking/raddock-overlaps-loadingpanel.aspx.
Basically, the idea is to set a z-index value for the UpdateProgress greater than the z-index value for the RadDock. Acording to the information provided in the link, RadDock has a z-index of 1000. So, setting a z-index value of 10000 for UpdatePanel solves the problem.