The applied date in Adagio comes straight from the document date of the transaction doing the applying - usually a check or a credit note. The system date has nothing to do whatsoever with anything.
Is your data clean? If it is and all of the transaction dates are in 2009, then you might need your Adagio consultant to look at this, using GridView. That program can dump data files into Excel, and with the Read/Write version can "fix" data such as a bad applied date.
Steve