This may be a day late and a dollar short for those of you who were looking for an answer, but for future seekers perhaps this will be helpful.
I was having an internal software error at the end of the Encore timeline. Having learned the hard way that things move quicker in Encore if you have your files already in .m2v with accompanying .wavs via AME, I figured everything would move smoothly. Naturally I was overly optimistic. For all its splendor, CS5 sure has some quirks. Anyway, my workaround (which presumably most of you have already figured out) was to start a Premiere project, import the .m2vs and .wavs onto one sequence, assign Encore chapter markers (if you want) and dynamically link the project to Encore. My project burned to disc without that pesky error the first time around.
Hope that helps.
Equipment:
Mac OS X 10.6.8
2 x 2.4 GHz Quad-Core Intel Xeon
12GB 1066 MHz DDR3
Adobe CS5