Initial valve clearance should be checked at 1000km, and every 4000km after. Your system uses shims, which makes it a bit more of a hassle to adjust. Here is a link to the MS3 250 service manual.
http://files.hyosungmotorsusa.com/MS...ice_Manual.pdf
If you have more than 1500mi on your scooter, this could be part of the problem. Having never adjusted a shim valve set, I can't be much more help, sorry.. but hopefully someone with experience on this particular scooter will jump in..