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The new Kindle Fire ad platform, which Kivin Varghese worked on at Amazon.

A former Amazon employee is suing the company over his termination, alleging that he was let go in retaliation for going over his manager’s head to bring internal attention to a “latency issue” that he believed would have “seriously jeopardized” the ad platform launch for the new Kindle Fire tablets this past fall.

The suit was filed Dec. 12 in King County Superior Court by tech and ad industry veteran Kivin Varghese, the former CEO of online ad startup BrandPort.

Varghese is seeking to invalidate an 18-month noncompete clause that was part of his Amazon employment agreement. His suit also asks the court to cancel his assignment to Amazon of an invention called the “Television Advertising Companion,” which predated his work at the Seattle company.

According to the suit, Varghese initially believed that he would be working on the ad platform for the Kindle e-readers, but was told after he started the job in March 2012 that he would actually be working on the then-unannounced advertising platform for the new Kindle Fire tablets. The complaint says he signed the non-compete and invention-assignment agreements when he was under this mistaken belief.

The complaint says, “It was only after he executed the Agreement and the Certification that Mr. Varghese was advised that the Amazon position for which he was hired was for the new, yet to be released, Kindle Tablet, a very different platform from the e-ink product, with completely different implications regarding the non-compete agreement, which were not apparent on the day his Agreement was signed.”

Much of the complaint centers on allegations related to Varghese’s manager, saying that she didn’t appropriately address a Kindle latency problem that he raised, required him to escalate the issue to an Amazon senior vice president. The problem was resolved prior to launch, according to the suit, which doesn’t detail the nature of the latency issue.

The suit also references an internal ethics complaint in which Varghese reported what he believed to be the “misuse” of hundreds of thousands of dollars of advertiser funds.

The suit alleges that Varghese was later terminated in retaliation for raising the internal complaints, despite Amazon policies encouraging employees to speak up in such situations..

Varghese hasn’t been shy about taking on large companies in court, suing Virgin Mobile in 2006 with allegations that the wireless company misappropriated BrandPort’s trade secrets after engaging in partnership discussions with his company.

We’ve left messages with Amazon and Varghese’s lawyer seeking comment on the suit, and we’ll update this post if we hear back.

(Thanks to Venkat Balasubramani for alerting us to the case.)

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