The Libertarians are not quite as friendly with the Republicans as many think. I believe that the Greens and Libertarians tried to get a recount in Ohio in 2004 because they alleged possible voter fraud. And I remember that one Libertarian coordinator urged Democrats to donate to the Badnarik campaign in a swing state [I think Wisconsin, can’t remember.] as a way to help the state go to Kerry.
Of course, you may be able to find examples of them working with the Republicans as well, but I think it depends on the circumstances. If there was a Democratic president up for reelection, they'd be more critical of him.
And Libertarians have complained to the NRA that they're endorsing Republicans over them. I think what got them so mad is that most Libs are more pro-gun than the average GOPer.