Hi Carsten,
The workspace preferences are stored in the workspace under ".metadata\.plugins\org.eclipse.core.runtime\.settings\org.eclipse.ui.workbench.prefs" file.
There is a bug filed against this issue already, SDSCM00047846.
If you want to default this setting for every new workspace, you can try adding the following line to the ccsv5\eclipse\plugins\com.ti.ccstudio.branding_xyz\plugin_customization.ini file. I haven't try it myself, so I am not sure if this workaround will work or not.
org.eclipse.ui.workbench/RUN_IN_BACKGROUND=true
Regards,
Patrick