Sorry for the inconvenience. If the value is of the format '1:00' then it wont be taken as a numerical value for creating a pivot table. This is a limitation now.
As a work around you can use formula as =HOUR(end-start)+MINUTE(end-start)/60 instead of just =(end-start) to get the value in numbers for pivot generation. Please try this work around and get back to us for further assistance.