Update to http://www.tesnexus.com/downloads/file.php?id=22163.
Version 2.2.0There are a total of 40 possible filters you can create. Each filter has 4 properties that control how it functions and what kind of map markers are affected. Now you can specify that a filter should only appear inside SI or only outside SI. So no more Oblivion Gates and Ayleid Ruins filters when you're in the Shivering Isles! Ofcourse configurable if you don't like it.

Here is a (short) description of each property:
_filterXtype = The map marker type that should be associated with this filter. See list below for numbers to choose from.
_filterXalt = Setting this to non-zero will associate this filter with another filter, the value determines which one. Meaning any map marker that would normally be controlled by this filter, will now be controlled by the other filter.
_filterXname = The name of the filter as is displayed in the Map Menu. Only applies if the filter is a new filter.
_filterXworld = When you want a filter to only appear inside the Shivering Isles or only outside of the Shivering Isles. Leave at 0 to always display filter, 1 for only inside SI and 2 for only outside SI.
<_filter1name> Camps </_filter1name> <_filter1type> 1 </_filter1type> <_filter1alt> 0 </_filter1alt> <_filter1world> 0 </_filter1world>
Default values are the same as standard DarNifiedUI map filters with the addition of the Wayshrines, Ayleid Wells and Magic Stones added by Map Marker Overhaul.
-kyoma