What is the difference between Machiavellianism and good negotiating/influence skills? I have been addicted to 'Great courses' books for some time now and have read quite a few books on influence, social skills, conflict management, negotiating, etc.  

Having basic knowledge in these areas I am now finding hard to see what is the difference between someone being Machiavellian and simply knowing how to negotiate, influence others. 

One could argue that being moral is what separates the two however knowing about cultural differences across the world it would be quite hard to draw a line (we burned witches after having 'magna carta' and developed judiciary system for centuries) plus would inevitably have to delve in to moral philosophy... and eventually pretty much would end up having to make judgments subjectively.

Is there an actual difference between Machiavellianism and good negotiating skills?
The term "Machiavellianism" can be used to refer to adherence to a set of strategies and guidelines for manipulation (eg, "personally deliver good news but have bad news delivered by others"), a moral philosophy (eg, "the means justifies the ends"), or a personality trait (also called "Machiavellian intelligence").  Since you've posted this question on a cognitive science forum, I will focus on the latter definition.

Machiavellianism is measured (as any personality trait), using a self-report scale.  This test, the Mach-IV, developed by Christie &amp; Geis (1970), does not measure negotiation skills, but mostly focuses on social and moral attitudes and beliefs.  As such, it would not normally be equated with any particular skills.

Fehr, Samson, &amp; Paulhus (1992) review 17 years of research on Machiavellianism, including its association with persuasion:


  Several studies have found that high Machs are particularly adept at
  persuading others in bargaining situations.


The review also mentions some notable exceptions, including a study by Fry (1985), that showed that a simple visual barrier greatly reduces the influence of high Machs.  A more recent review by Jones &amp; Paulhus (2009) also agrees:


  ... high Mach IV scores do predict who will and who will not engage in
  interpersonal manipulation.


So although the term refers to a set of self-reported attitudes about social relationships, and not a measure of any particular skills, it would be reasonable to say that Machiavellianism correlates with negotiation skills.

For completeness, I should mention that the strong correlation is not an accident.  In fact, as the review points out:


  ... the construct validity of Machiavellianism rests largely on the
  match between high Mach IV scores and actual pragmatic manipulation.


In other words, the test was written and adjusted to have this correlation, so it may be more accurate to say that Machiavellianism is validated by negotiation skills.