I'm not sure why you get that problem, but perhaps someone else can comment in that. Re-configuring the link is easy though, and should hopefully solve the problem.
Windows
Go to "Tools" in the "options" menu. Choose "Mathematica" under "Global" and then "Configure SystemModeler Link...".
OS X
Go to "Preferences" in the SystemModeler menu (shortcut: ?,). Choose "Mathematica" under "Global" and then "Configure SystemModeler Link...".
Linux
Probably the same as Windows, but as I'm not running Linux I don't know the details.
Tips & trick
Independent of the OS you use, you can click on the cog wheel in the bottom right corner of the class browser to get to the options/preferences window.