Here is the line I'm passing to it via command line:
sampleclient -host 10.10.1.1:800 "C:\TEMP\script.jsx" arg0="C:\TEMP\file.indd" arg1="C:\TEMP\file.pdf"
Now I'm passing this:
sampleclient -host 10.10.1.1:800 "\\server\temp\script.jsx" arg0="\\server\TEMP\file.indd" arg1="\\server\TEMP\file.pdf"
And it gives an error 48 - Cannot find a folder.
Is that \\server mounted on both machines?
sampleclient allows to specify the script either as file in its own file system (your case, it would be uploaded with the soap call), or as file on the server machine (specify the "-server" argument).
Another wild guess (I mainly work with Macs) is the backslash, it could be interpreted as escape character, in that case you'd have to double it.