Yes, this appears to be at least partly true.
From a column by Todd Starnes in Fox News Radio:
“Little girls should not be exposed to naked men, period,” said David Hacker, senior legal counsel with the Alliance Defending Freedom. A group of concerned parents contacted the legal firm for help.
Hacker said a 45-year-old male student, who dresses as a woman and goes by the name Colleen Francis, undressed and exposed his genitals on several occasions inside the woman’s locker room at Evergreen State College.
Students from nearby Olympia High School as well as children at a local swimming club share locker rooms with the college.
According to a police report, the mother of a 17-year-old girl complained after her daughter saw the transgender individual walking naked in the locker room. A female swim coach confronted the man sprawled out in a sauna exposing himself. She ordered him to leave and called police.
The coach later apologized when she discovered the man was transgendered but explained there were girls using the facility as young as six years old who weren't used to seeing male genitals.
Later in the same article,
“Clearly, allowing a person who is biologically a man to undress and expose himself to young girls places those girls at risk for emotional distress and harm,” [Hacker] wrote in a letter to the college. “Any reasonable person would view this as dangerous to the young girls involved. The fact that this individual was sitting in plain view of young girls changing into their swimsuits puts you and Evergreen on notice of possible future harm.”
Starnes' article (going by the comments, dated November 1, 2012) references an October 5, 2012 news report (and video) by a Seattle TV station named KIRO-TV which might be the original source. The Kiro TV report however makes no reference to six year olds and only notes that high school swim teams use the facilities. Even the lawyer quoted in the Starnes article only mentions "young girls" being exposed to male genitalia presumably referring to the (17-year-old) high school girl(s) in the incident; only the apologetic swim team coach brings up six-year-olds being potentially exposed.
Going by the fact that a "group of concerned parents" took legal counsel, we can probably conclude that there were a number of complaints made to Evergreen State College. However, there do not appear to be any online reports (or updates) on this issue after November 2012 which suggests that there haven't been any further complaints.
This makes Tami Fitzgerald's February 2015 claim (in the OP) of "frequent complaints about indecent exposure in front of girls as young as 6 years old" very likely a gross exaggeration.
Other articles on this story include those on Seattle Weekly, an ABC News blog, and a piece (with pictures) in the UK's Daily Mail. Some of these articles refer to a Komo TV report (that I have been unable to unearth) which might have more information.
P.S. While I am unfamiliar with the process, comments below the Kiro TV story note that Colleen Francis appears to be undergoing hormone replacement therapy and a side profile in the video does reveal significant breast development.