Is there a difference or are they synonyms?
Bybee, Pagliuca and Perkins 1996 put it very nicely. Here's what they wrote.
Iterative "signals that an action is repeated on a single occasion and differs from the habitual and frequentative, which both signal the repetition occurred on different occasions" (p. 160). Here are the two examples they use:
He searched for his keys all morning. iterative
He searched for his brother in every city he visited. frequentative
Naturally, there is a lot of variation in linguistic terminology, esp. in aspect studies. Comrie 1976 argues for the importance of the iterative vs. habitual distinction; thus, the frequentative is viewed as a subclass of the habitual. Carslon 2012 does mention Van Geenhoven 2004, who views the frequentative as a subclass of the iterative; however, Carlson insists that Van Geenhoven 2004 terminology is not general usage.