Mendix does not support running on a database with other, non-Mendix tables. Tables like 'sysarticlecolumns' are not default SQL Server system tables, but they are added when the database is used as a publisher in a replication architecture. Such tables will be removed at this moment.
Mendix will respect the replication tables in the next maintenance release (2.5.5) and in 3.0 of course.
Sorry for the misunderstanding but in that case it would be good if you would provide some more information and maybe include the error message/stack trace. You should also create a ticket at the partner portal.