lol ok, fixed version (hopefully) was just uploaded
http://multimame.wikidot.com/start so test that if you don't mind.
But yes, you will want it to filter on just the ONE game.... because currently you will always use one or the other.
in the filters page on multimame
"INLIST will allow you to add a comma delimeted list in the <Value> of game names (rom names) you want added or removed. This allows you to configure some items by hand"
so I believe it will be
<Filter>
<Name>Single</Name>
<Emulator>Misfit</Emulator>
<Hide>false</Hide>
<Conditions>
<Condition>
<Value>pachackversion, pachackversion2, rygarhack</Value>
<Operator>INLINE</Operator>
<And>false</And>
</Condition>
</Conditions>
</Filter>
Sadly, I don't remember if this should be before or after the other. I believe it should be second, so it replaces the version in mame if there was one.
And after all this, if you changed the name (<Name>ALL</Name>) to anything else, I think it would have worked without the new version... oh well...