Did you alter your payroll system to allow for the additional time period?

AFAIK, ours is set to weekly and bases its PAYE calcualtions on the assumption that the amount paid if for 1 weeks wages, it then uses the tax tables to pay from that (Ace Payroll). If I paid 3 weeks worth of pay but didn't tell the system it was for 3 weeks, then yes, I'd expect it to take more tax.

I did ours on Tuesday, but processed 3 separate pay runs, forecasting each week until I return in January, that way each wage run was still in line with the payroll processing period.