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The behavior you are observing is correct.
When a job is dispatched, the pre-exec/job/post-exec will all run in the specified cwd. The check for whether the cwd actually exists is done the first time something tries to access it.
In your case, the pre-exec tries to run in "c:\temp\abaqus\username\projname" which does not exist at that point, so execution defaults to tmp. The pre-exec succeeds and the job is executed in tmp.
If you use a dynamic pattern for the cwd, then the directory will be automatically created before the pre-exec runs.
For example, bsub -cwd "C:\temp\abaqus\%U\projname" -P "projname" -E pre_exec.bat abaqus file.inp
%U is replaced by the current username, and the directory will be created prior to the pre-exec running.