Markit is the parser that Arbortext Editor uses to validate documents. The inability of Arbortext Editor to find Arbortext-native files often occurs when you use an APTCATPATH environment variable that does not contain %D as one of the paths. (%D is the default path to Arbortext's own catalog files.) Your APTCATPATH variable value should read something like: C:\mydocuments\mydoctype;%D Leaving out the %D (don't forget the semi-colon separating it from the previous path) would cause this.
We also had the markitx issue when we first started with ArborText. Our fix was to give the user full permissions to the "C:\temp" folder which AT was using. Apparently, markitx is associated to one of the temp files AT creates and then reads and then deletes. When the user did not have Read and Write permissions, AT would return the error you mentioned.