For CUPS to count correctly, the printfile needs to pass the CUPS pstops filter; otherwise it uses a dummy count of “one”. Some print files do not pass it (e.g., image files), but then those are mostly one-page jobs anyway. This also means that proprietary drivers for the target printer running on the client computers and CUPS/Samba, which then spool these files as “raw” (i.e., leaving them untouched, not filtering them), will be counted as one-pagers too!

You need to send PostScript from the clients (i.e., run a PostScript driver there) to have the chance to get accounting done. If the printer is a non-PostScript model, you need to let CUPS do the job to convert the file to a print-ready format for the target printer. This is currently working for about a thousand different printer models. Linuxprinting.org has a driver list.