[isabelle] Jedit: Spurious "Bad Theory" error

Refering to Isabelle2013-1-RC2:

When loading some big development in jedit, e.g.,
JinjaThreads/JinjaThreads.thy, it prints an error message "Bad
Theory: .../Basic_Main.thy" and has an error marker (red underline) on
the first line (theory JinjaThreads) of "JinjaThreads.thy". 

After a few second (30 or so, the error marker disappears), after a few
minutes, also the error message in the output disappears.

This behaviour is really puzzling, I was already wondering what went
wrong here, until somebody told me that it is normal for jedit to print
some error messages on correct theories, that then magically disappear
after some time.


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