The census will calculate the student numbers on the day of the census (even if you are running your census after census day.
If you go to Reporting >Reports > Students (tab) > On Roll by Date and enter the census date, you can see the numbers ScholarPack will be using on the day of the census. Check the numbers per year group to see if there are any irregularities. It would be worth focusing on new starters and those who have gone off roll recently to check if entry/leaving dates are correct.
It's also worth going to Admin > Students > Group Updater and checking the student attribute of Hidden Pupil. Any student who is set to Yes for this will be excluded from all census calculations, including on roll figures.