I know i am late . But for anyone else who in future faces this issue.
I tried retrieving a table from the export parameter of function module in the web service.
eg. <LtFlight/>
The FM was working perfectly but returning an empty reponse in the service.
I then removed the export parameter and instead added it in TABLES .
eg. lt_flight like str_flight (where str_flight is a structure)
And this worked.
The web service was now able to get all the data as required. 
Hope this helps.