Bob,
I think you will find that no agency will pay the pilot until the airline pays the agency. The more honest agency will include such a clause in their contract, if it is there, do not be afraid, at least they are being honest about it but do establish for how long they have been dealing with that particular airline and of any history of non or late payment(s).
The less than honest agency will not declare such a clause but at the end of the day, bearing in mind the agency may be working on a 10% fee, they will not be in a position to subsidise the airline's payroll for a month (equivalent to 9 months of fees for them) thus the chances of the pilot getting paid, well you work it out!