Each entry will need to have qualifiers in the item name. Base qualifiers are the format type, until box variations are considered.
So the existing entry (40270) should have (CD) in its title. And the version you have should indicate the media type...
You can use these entries for Pirates! Gold as an example:
http://vgcollect.com/search/advanced/8/pirates%20gold/no-filterNote: the 2 Win95 entries are not dupes.
But really, the PC categories need to be split up as that is too generic of a category. There are over 200 pages in PC [NA] and I would bet we have 20% (I really want to say 5%) or less of PC games in the db.