The browser used and the version of the browser would also be helpful. The reason that I bring this up is that a similar issue with the left navigation menu not working was seen with one of the older example implementations of mashup gadgets (the example implementation is a few years old). This problem only occurs with some modern browsers but not with older browsers or with IE when compatibility view was used.
When you want to display a full portal with a mashup you can't simply use the PegaA="display" and display the portal harness. The portal has not been fully initialized. What you are seeing is common behavoir when use PegaA="display" and an end user protal harness.
To properly display a end user portal use the following :
when the gadget loaded first time, the left nav links are working but when we close any opened document(open and close a case, open the harness and close using the close button) then left nav links are not working.
if we refresh the screen then the links are working.