We experience the same intermittent behavior, with JavascriptMVC 3.2 (pre-CanJS) on OSX. We're using the multi-build feature on around 20 apps, and when it occurs, one of the apps will not be packaged. It seemed to only occur on the apps with the most dependencies.
Unfortunately it was quite a while ago, so I don't recall all the details - we now use a dirty-but-practical workaround:
We use a Python script to execute the build command (e.g. `./js steal/buildjs myproject/app1 myproject/app2 myproject/app3`) and capture the output to stdout into a string.
When the build completes, the Python script checks that captured output for the presence of each of those app names (`myproject/app1`, etc.) and retries if any were not present. This works because part of the output (for our version of Steal, at least) describes which apps share each of the packages.