The more frequent problem is not to see the changes in Encore. This is usually because the project had already been transcoded, and changes in Premiere only come through after you use "revert to original" to tell Encore to no longer use the transcoded files.
The fact that you see the changes suggests this is not the problem, but check to be sure.
Prior to CS6, this happened with BD builds, and the solution was to clear files Encore used for b uild.
http://forums.adobe.com/thread/670174?tstart=0
But as of CS6, this step was done automatically, and as long as your build completed, you should not see these files.
You have not actually told us that the changes are to a timeline rather than a motion menu, but I assume it is a timeline.
When Encore continues to see an old version of a timeline rather than the new one it displays in preview etc, the project may be corrupt. Sometimes it cannot be salvaged and must be started over. Sometimes you can help Encore see the light by clearing the cache or similar.
These are dated, but most still applies.
Troubleshoot damaged projects in Encore on Windows
http://kb2.adobe.com/cps/406/kb406006.html
Troubleshoot system errors and freezes | Adobe software on Windows
http://kb2.adobe.com/cps/822/cpsid_82252.html
Troubleshoot system errors and freezes | Adobe software on Mac OS 10.x
http://kb2.adobe.com/cps/824/cpsid_82414.html
You reported good information (version of Encore, version of Premiere, use of dynamic link). It may not matter here, but it is also good to report the operating system (Mac vs PC, and OS version for either) and full version of Encore (e.g. 6.0.2.004 is the latest).