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The only real differences between running the CVS action in VBP and running CVS command-line directly outside of VBP would be the current directory of the process and its environment settings.
The CVS action will set the current directory for the process to the value provided in the Path field on the Repository tab, so make sure this matches the path you are running your Command Prompt test from.
You could compare the environments by building a Run Program step of
%DOSCMD% set
and comparing the output with a 'set' command from your Command Prompt to see if anything it different.
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