Hi Anuar,
As far as I am concern, there is only one agreement, ie Tenancy Agreement between Landlord and Tenant. By standard practice, the commission is 1 month for a tenancy period of 1 year. A higher commission of 1.25 to 1.5 months apply to tenancy period of 2 years and above, and the commission rate differs from one agency firm to another, and depends on the landlord's persuasion for a lower rate.
There is a separate charge where the tenant needs to pay. ie. to execute the tenancy agreeement and it is called Stamping Fee. The agency may also charge a separate fee for "preparation of tenancy agreement" and I believe the rate varies with each agency. It is pretty subjective.
Where as, for the tenant to pay RM500 for renewal, IMPO (In my personal opinion), I think this is not the norm. It is pretty common for renewal that landlord pays 1/2 month to 1 month, but I have never heard of tenants paying for renewal.
BTW, if your rented unit is RM1000, and the same amount is stated in the Tenancy Agreement, it shall not exceed this amount for rental chargeable to the tenant, on what was agreed at the first place. If RM1000 is collected on behalf of u, and RM900 is returned to you, the RM100 should be treated as an overiding commission to the agent, and you both should have a simple agreement on this.
Hope it helps.