RedCardinal - 9:53 am on May 18, 2012 (gmt 0)
I'd say the Penguin filter simply isn't running when you use a specific modifier.
For me this only seems to works with modifier strings that would affect the domains being listed. So [query -waffle] shows Penguin results, but [query -co.uk] shows results sans Penguin. Trying [query -.fr] shows Penguin results, and I can only guess this is due to there being no .fr results in the set.