Of course it does, that's How It Works regardless of application.and executes the first it finds according to the Windows system PATH.
This is a known issue with a known solution which has been posted both here and at the IBM site from what I recall. It's not a 'DataStage bug' but a PATH problem, so making sure the 'proper' directory is in the search path first (or at least before any 'improper' ones) will solve the problem. This would be true for any issue of this nature.