I have upgraded my Force.com IDE to version 31. This added the below permissions to my existing custom objects
<enableBulkApi>true</enableBulkApi> <enableSharing>true</enableSharing> <enableStreamingApi>true</enableStreamingApi>
Now after committing when I deploy my code to a new org and login as System administrator the fields are not visible . I have to manually give the fields permission. This issue is occurring with existing objects.