One of these packages must have obtained an higher priority than CYVR in the scenery library, because you don't just have double marking, you are missing all the custom ones that comes with CYVR, meaning two sceneries are covering it.
You need to be sure FSDT CYVR is being loaded last, with SU10 you can use the Experimental menu to use the new tool to rearrange the various scenery areas.
