The troubleshooting approach depends on whether you are on deadline. If so, replace the dynamic links with exports from PR. Use replace asset.
Otherwise, try these 2 links:
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
Be sure you are updated to Encore 6.0.2 (for windows).