IDE Version 1.6.4 vs 1.5.4 for Yun

Can anyone tell me why the application that I developed in version 1.5.4 for the Yun that works great will not work in version 1.6.4? Compiles fine, uploads fine but does not actually function when the program runs. It does some very strange things. The Ethernet Bridge will not connect and the IO do strange things.

Any idea why this might happen?

Thanks!