I just thought I'd let you know we've seen the exact same behavior.
I've just done a bit of playing with this.
Firstly, there's a couple of scenarios where this is expected:
1) If you modify one of the default queries, but don't change its name, then a new query will be created (as you don't want ePO to overwrite your modified query and set it back to default.)
2) If the extension is removed, and then checked back in (or a new version is checked in) then this will happen: removing the extension doesn’t remove the queries, and the new checkin will create duplicates.
That said, it looks like there's a bug in the patch 3 (18.104.22.168) viruscanreports extension. It appears not to contain the correct information for thefollowing queries:
VSE: Current Dat Adoption
VSE: Number Of Detections By Tag
VSE: Top 10 Buffer Overflows Detected
This means that if you check this extension in over the previous version, even if you haven't modified these queries, the extension doesn’t recognise them and so creates a duplicate.
If you haven't already done so, please open a case with Support so we can get this addressed.
I will create a SR to this, and wait for the solution to this particular issue.
Thanks in advanced.