Hi Mark,
Is your medical expense paid by your employer or from your pocket?Are you hired by the agency or your employer hired you directly and they just need an agency to process your exit clearance? If you are hired directly by your employer and they paid for your medical expense, then it would be better to raise this issue to your employer. On the other hand, if you are a direct recruit by the agency, i would suggest you follow their advise as they have their own policy also in terms of recruiting a filipino worker.You have to understand that it's their responsibility to the Employer and to the Government to deploy a "Fit to work" person that is why "Maybe" they require you to take a medical exam twice.