Ok, managed to solve my own problem by reordering the datestamp string using the following code:
yyyy = identifier.timestamp(1:4) % Sets yyyy as the year
mmdd = identified.timestamp(6:10) % Sets mmdd as the month and day
mmddyyyy = strcat(mmdd, '.', year) % Concatenates strings 'mmdd' '.' 'year'
mmddyyyy = strrep(mmddyyyy, '.', ',') % Replaces all '.' with ','
datenum(mmddyyyy)
This now gives me a correct number for the date provided in the timestamp. So for 01,01,2009 I get 733774.