I have found my answer.
To work around this , any classes that you need to access the file system must be in the ext folder under the J9 folder.
In my case i was using microlog as my logging solution and was looking to create the files. My applications jar was not in the ext folder, so i repackaged everything so that the java classes for the appenders were in the ext folder so that they were considered to be bootstrap classes by the j9 jvm.
If anyone has any questions please ask them in the comments.
thanks to all who looked at this.