Export a 10 minute test piece from Premiere, and import as timeline to Encore. Be sure you are using H.264-Bluray and not just H.264.
Is your export format supported?:
http://forums.adobe.com/message/1901666#1901666
Does Encore show "do not transcode" under the Bluray Transcode Status?
Since you are using CS5.5, consider the possibility that you are affected by the H.264 2 pass bug. Fixed in CS6 I think.
http://forums.adobe.com/message/3876184
However, see post 20 in the following link, where Jeff Bellune is suggesting (I think) that this may not be a single 2 pass vbr bug, but a relationship between the profile also.