i did a little further investigation. This command stcmd diff -p "user:password@domain:port/project/view/parentFolder/subFolder/subFolder1" -vn 4 -vn 1 "fileName" should work with both the 12.5.0.31 & the 12.5.0.40 versions of the SDK. Since you are unable to get it to work, I suggest you raise an issue with Customer Support. You may either provide them with your StarTeam database (if they don't have it already) or provide them the steps to replicate the problem from first principles. Once they reproduce, it becomes an internal engineering problem, we'll investigate, fix what's broken and and then issue a new build (both 12.5 & 13.0) with the fix.
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