Both sides have the same enemies. the ADL, the SPLC, the government, the media.
I would say Stormfront and the liberty movement agree on 80% of the issues. The main issue separating the two are whether race plays a factor in politics or not. Although I suspect most liberty movement people realize this but simply are cowards who won't say so. It is clearly an ethnic-movement based on demographics alone. Also, people don't have the freedom to discuss the jewish question without respecting certain politically correct norms in the freedom movement. Other than these two issues, there isn't a dimes worth of difference (although some would argue it is a big difference).
I can see why the enemy would like to draw a connection between the two. Their insults are best ignored. You can't win a battle about why you aren't a racist. You simply look like an idiot. Ron Paul begged and pleaded to not be a racist in the last election. I lost a lot of respect for him when he did that. You're better off giving them the finger than fighting.