Hi,
as written in FS/CIVA/DOCS/ACTION AND MALFUNCTION CODES the code 06-41 appears when the inserted present position differs more than 3NM from the parking position where the plane arrived in the  precedent flight.
In the realty hardly ever the plane changes parking gate during the stops in the transit airports and, on the other hand,the tolerance of 3NM  is quite enough to cover all plane movements in almost all world  airports.
But within FS simmers change flight at every session and almost always the Departure gate position differs more than 3NM from the precedent arrival gate position.
Don't consider 06-41 as an error but as  a warning and it can be cleared clicking over the TEST INS button as required.
If you're departing from the same gate where you arrived in the precedent session and 06-41 codes appear, give a look at the inserted gate position maybe you've  made an unintentional insertion mistake.
Regards Gianfranco