Is the Employee_ID field marked as a Global Filter inside the workbook itself? If it is, setting the value of the filter in any of the sheets should affect the others (as far as I know). Are you seeing something different?
Yes, it is currently set as a global filter.
Odd, this works for me. Are you on the latest/greatest version of Server?
tabcmd export "Book4/Sheet1?ProductCategory=Furniture" --fullpdf --pagelayout portrait -f "c:\test.pdf"
....against the attached workbook, and the PDF which was returned (also attached) was filtered appropriately - only "furniture" values vs. technology & office supplies.
Can you upload a sample that isn't working for you?