A follow up to this thread (https://forum.simutrans.com/index.php/topic,22955.0.html), looks like the folder bug had been fixed but another show up. I noticed when my option setting does not save after I close the program and restart. Turns out Simutrans does not use Documents folder in Windows instead it saves in the program folder as I can't find the save file nor screenshot in the Documents folder.
Are you sure, you did not try a portable installation into the Program File directory? YOu can check if there is singleuser_install = 1 in the file config/simuconf.tab
Setting this value to zero (or install Simutrans again with making sure not clicking on portable installation) should fix this.
I checked the config and yes, singleuser_install = 1. I must have accidentally set portable install during update. The issues had been fixed, thanks prissi.