no particular affect to PR application
By contract means the company needs to re-offer you after the contract expire. It has no particular affect to your PR application, unless it is too shorter (saying less than 1 year).
temp/contract/permanent
If you are under contract, the employer can opt not to renew the contract without giving any reasons when the old one expires, which means you lose the job without any compensation.
If you are under permanent employment, the employer can still fire you but probably need an excuse and you will be somewhat comepensated for it.
There are other benefits that only applicable to Perm staff like extra medical/insurance coverage, long sevrvice award etc.