In Command Workstation, we always import jobs rather than sending a pdf using the driver. We noticed a color difference early on and saw we needed to be consistent.
Are you talk about using CW, going to File>Import Job? I currently just drop PDF's in CW. Does CW handle the PDF's differently by importing rather then dropping them?
Yes. We have been importing pdfs that way for five years. We tried using the hot folder at first but it wasn't working for us. Believe it or not, we still are using CW4, since shortly after the install, CW5 crashed and we couldn't get it back. Maybe CW5 has improved the ability to drop files -- I don't know. Anyway, CW4 has been tried and true for us.