dear josidon,
as far as i know, your tarnsportation allowance is one of your basic benefits as long as you are on duty.
i mean that your employer is not obliged to pay it during your PTOs..... actually you wont find any article in labour law implying single term for the same but mostly it should be clearly mentioned in your companys compa & benefis policy.
and for my friend who said that his company does not pay him transportation allowance, i believe that he can claim for it even if it is not indicated in his contract, coz this is an obvious breach of labour law & concession for the employee.