Are you saying that you did not install the whole MC? Have you installed at least Premiere and Adobe Media Encoder?
I wnder if there is an install issue. Encore is only provided with Premiere, and I don't know what happens if it is installed without it.
If that is not it, look at this. It is not specific to Encore, but may be relevant.
Troubleshoot system errors and freezes | Adobe software on Mac OS 10.x
I do have the Master Collection installed otherwise, including Premiere Pro, and After Effects (along with Media Encoder, etc.). I needed to install Encore CS5 for a school project, so I installed it in addition to the rest of the suite. Should have clarified that earlier, sorry!
Thanks for the clarification.
I would try 2 types of things.
First, look at the type of Encore project you are creating. DVD vs Bluray; default transcode settings. Also whether you have a blank disk in the drive (don't).
Second, try the simpler things in the link I sent. Permissions and the like can be issues.
Also, Lion had some issues, but I only recall them in other apps.