Zynga’s Owen Van Natta has stepped down from his post as Executive Vice President and Chief Business Officer to become a strategic advisor, handing back millions of pre-IPO shares, according to a new amendment to Zynga’s form S-1. Other changes include director and venture investor Brad Feld leaving the board while Spring Ventures partner Sunil Paul joins it.

It’s tempting to read into Van Natta’s move, given that he’s moved from a senior role at Facebook to CEO of MySpace for less than a year, and is now coming down from his EVP & CBO role at Zynga after 14 months. According to a statements made to AllThingsD, however, that’s not the case. Unnamed sources also tell the blog that Van Natta’s move has nothing to do with a recent stock scandal where The Wall Street Journal reported that Zynga was attempting to redistribute shares among its employees. Additionally, CEO Mark Pincus said for the record that “Owen is a valuable business partner. He’s made great contributions to Zynga and continues to be an important part of our team.”

As for Feld and Paul, the timing is not altogether strange for a VC sitting on the board of a company about to go public. Paul fills his place, having previously worked with Pincus on founding a company called FreeLoader, which sold for $38 million in 1996.

Zynga’s IPO is expected to happen before the end of 2011.