Which platform are you having issues with and how did you install the plugin? At the moment, I can't get the latest version of inappbrowser to install via "cordova plugin add org.apache.cordova.inappbrowser" - it gives me installation errors. Instead I have to force install of the 0.3.0 version to get the install to run properly in the CLI: "cordova plugin add org.apache.cord...@0.3.0"
If you use "window.open(url, '_system');" and it opens in the app's window, then the inappbrowser plugin is probably not installed properly.
Perry