Used PDOC last year to calculate payroll. Remittances are not the same. HELP!

I used the PDOC from Revenue Canada to calculate my 2015 payroll. Prior to this, I had a sage payroll subscription so it auto calculated everything so this issue is completely new to me. All of my employees are 18 or older with the basic 2015 personal amounts of $11,327 Federal and $18,214 Alberta. This is entered in sage in their payroll files, as well as our 12 pay periods per year. I have been using sage to add all my 2015 data so I have a proper record of everything. I do not subscribe to a payroll service plan with automatic calculations anymore because PDOC did the calculations for me last year already. I simply pay Sage to gain access to the payroll module and manually enter pay checks and tax information to match what is on the PDOC statements. I am currently operating the 2016 version in order to keep the payroll module accessible, but working in calendar year of 2015.

Despite the fact that all my personal amounts are correct, number of pay periods is correct, and everything in the pay check window exactly matches the amounts on the PDOC generated summary in terms of fed/prov taxes, CPP, EI.... when I use the "Pay Remittances" window to post my remittances on the dates that I paid them, the amounts calculated are not the same as the ones that the PDOC statement says to remit. Sometimes by a fairly large margin - and not just by a few cents or dollars.

At the bottom of each PDOC slip, for each pay check I process it says "Remit this amount". I have totaled up the amounts for each of the periods in 2015, and when added together  my total remittance for any particular period has been nowhere near the amounts in the "Pay Remittance" that Sage has come up with. As much as $340 difference in some remittance periods. I have no idea why this is when the deductions are all identical and claim codes are entered as they should be. Why is there such a discrepancy, and how can I correct it without making an even bigger mess?!