112madgamer, let's not use Registry methods for Ragnarok because it can be solved without it. I've played Ragnarok for years, so let me deal with that.
Vlin, that's happening because the wrapper needs to know where is the game exe, and since you are installing a different server the exe path is different. You need to right-click the game in your local tab, press Properties, click on Advanced and click on Browse on the Main EXE field, selecting the exe that runs the game.
About the Resolution, you should set it on Setup: You shouldn't set the resolution throw the Porting Center, you should adjust the Setup app path to select Ragnarok's Setup. After that, you will be able to run it using an alias/shortcut which will be in the game folder, and use it to change the game resolution. If you can't find the Setup app, open Porting Kit and go to the local tab. You will find it there, since that port was made to create it too. If you can also find it there, right click the game on the local tab, press "Show Package Contents" and double click the Setup app.