No, it is not a directory you are misreading the \" at the end of the command name:

"c:\path\cleartool" -fmt "%[owner]p" vob:.  #outside perl
[download]

\"c:\\path\\cleartool\" -fmt \"%[owner]p\" vob:. #inside perl
[download]

The problem is that something is eating the first quote at the beginning of the line and the second quote in the parameter section, instead of either eating matching quotes or leaving them alone.