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That is strange. The only differences between using the SourceSafe action / SSHELPER and calling ss.exe directly are:
1) By default, they auto-locate the ss.exe to invoke. If you check the 'show command-line' option on the Options tab (for the SourceSafe action), build again, and it is invoking a different ss.exe than your working test, you can override that by explicitly specifying path+filename for ss.exe.
2) Setting the SSDIR environment variable before invoking ss.exe to point it to the correct database. You don't indicate whether you're doing this in the case where you invoke ss.exe directly. If not, your command may be operating on a different database; if you call
SET SSDIR=y:\path
in your Command Prompt before the ss.exe command, that should ensure an equivalent comparison.
3) Setting the current directory to the path in 'Path for local files' field.
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