You'll need to format the hours separately, as below, since style "114" will only handle up to 23 hours:

SELECT

CAST(DATEDIFF(ms, ActualStartTime, EndTime) / 3600000 AS varchar(3)) +

RIGHT(CONVERT(VARCHAR(12), DATEADD(MS,DATEDIFF(ms, ActualStartTime, EndTime), 0), 114), 10) AS ELAPSED

FROM (

select cast('2013-09-13 17:49:36.000' as datetime) AS ActualStartTime,

cast('2013-09-14 12:40:47.000' as datetime) AS EndTime

union all

select '2013-09-30 00:22:05.000', '2013-10-01 02:04:51.000'

) AS test_data