More information needed for someone to help... click these links and provide the requested information
Information on what you are editing... what you export from PPro... your Encore project... screen shots help a lot
Read Bill Hunt on a file type as WRAPPER http://forums.adobe.com/thread/440037
What is a CODEC... a Primer http://forums.adobe.com/thread/546811
What CODEC is INSIDE that file? http://forums.adobe.com/thread/440037
Report back with the codec details of your files, use the program below... a screen shot works well to SHOW people what you are doing
Export directly from Premiere to H.264 BluRay (better codec then mpeg).
Import the two files into Encore.
See how that will work for you.