I discovered today that you cannot build our EsiPlatformDataDS project from within BEA workshop after performing a 'clean'. The error is 'package commonj.sdo does not exist'. If you run our automated build within Eclipse for that project, then BEA workshop will start working as well -- until the next 'clean'.
Further investigation is needed to figure out why this is happening.
On a related note... don't give BEA Workshop focus while running a build of the application from outside (e.g. from within Eclipse). If you do, then workshop will note that project files have changed and will kick off a build of its own. The two builds will conflict and neither will work properly.