LGF [1] links to an article on Sultan Knish [2], blockquoting this text from Knish:

“No one is perfect and I am certainly not. I think my former posts on the topic were fairly realistic about what to expect from some European conservatives. And then Brussels Journal put up one post promoting Ron Paul as the American Paul Belien and an article from Taki’s magazine that cheers Jewish Holocaust denier Norman Finkelstein as an inconoclast, calls Mearsheimer and Walt “illustrious academics” and claims AIPAC was behind the invasion of Kuwait.”

Certainly sounds anti-Zionist, if not anti-Semitic. But you go to the actual BJ post [3], the relevent section reads:

“It might also be asked why the Israelis, who run a Western-type constitutional government, should trust the Palestinians politically – even if admittedly Israeli military forces have sometimes taken brutal revenge on the Palestinians after Hamas-incited terror-bombings. There is nothing in the Palestinian, or for that matter the Arab Muslim, past that would suggest the likelihood that they would honor and enforce treaties or control violent minorities that might seek to wipe out the Israelis. I am always amazed when my friends on the right who, although justly skeptical of the belief that Arabs Muslims could develop Western-type regimes, express every confidence that the Palestinians are closet-moderates. All that is needed for the unexpected to happen is for the Israelis to give the West Bankers a chance by clearing out of the West Bank and by giving the Arabs control of East Jerusalem.”

BJ's excerpted pro-Zionist sections of the original post! [4]

If LGF has a point, denying science and distorting the textual record isn't a logically valid way to get it across — though it may help score rhetorical points.

[1] http://littlegreenfootballs.com/weblog/?entry=27925_Sultan_Knish_Speaks&only
[2] http://sultanknish.blogspot.com/2007/11/well-im-done-defending-brussels-journal.html
[3] http://www.brusselsjournal.com/node/2667
[4] http://www.takimag.com/site/article/mopping_up_the_israel_lobby/

What it all really stemmed from was Vlaams Belang's (and Swedish Democrats) relations with the White Power movement (and even Nazi sympathizers) and other far rightest groups in Europe. There is overwhelming evidence of such links and sympathies and no overt denunciation of those links. LGF made the point that it was important not to let the far-right hijack the anti-jihadi discourse.
The main gist of the allegations have never adequately been addressed by the guys at VB, IMO:

http://littlegreenfootballs.com/weblog/?entry=27784_The_Mask_Comes_Off_at_Brussels_Journal&only

http://babbazeesbrain.blogspot.com/2007/11/now-is-dewinter-of-our-discontent.html

Thank you for your clarification. The context I had for understanding the controversy was the LGF comment thread.

I am unaware to the extent that European conservative movements purged extremists, in the manner that WFB Jr. led the purge of the Objectivists and the Birchers. So with respect to extremist fellow travelers among European conservatives, I have to plead ignorance.

This caused some people to start accusing LGF to be in camp with the jihadi sympathizers, which was ridiculous. However, in light of the strong reaction Charles Johnson started digging at the background of the groups and came up with some pretty damning stuff. What's worse is that the leader of Vlaams Belang will only give shifty answers to the charges, all of which can be heard in an interview he gave to the Shire Podcast (which caused a split among those guys):
http://littlegreenfootballs.com/weblog/?entry=27736_Vlaams_Belang_Leader_Interviewed&only

As LGF kept digging, more stuff came up that showed that the members of VB associated or had associated with those who espouse the White Power or White Nationalist cause and symbols. For instance Filip Dewinter has an Odin's Cross on his bookshelf, a symbol that has become a sort of hidden swastika.
All this has caused splits among many bloggers and personal attacks upon Charles Johnson, but precious little in the way of answering some very reasonable questions about the associations and beliefs of the leadership of VB. Not surprisingly, if one looks around enough, it not just one Abrahamic faith these guys don't like.

I agree with Charles Johnson that the last thing the anti-jihad types need is to be associated and hijacked by a bunch of thugs with ulterior motives and dishonest leaders.

http://gatesofvienna.blogspot.com/2007_11_01_archive.html

http://conswede.blogspot.com/
http://1389blog.com/2007/11/24/it-is-time-to-punt-little-green-footballs/

http://1389blog.com/2007/11/27/little-green-footballs-hitting-new-lows-one-after-another/

There is no smoking gun, but there is a loosy-goosy relationship among the right in Europe, including Vlaams Belang, with those who are not [classically] liberal. Too many people throw out the racism card if you start talking about Islamism as a threat, best not to get tarred by unwelcome fellow travelers.