A federal investigation of Pacific Investment Management Co. is the latest crack in the armor of the $2 trillion fund giant, where a trustee recently questioned the $200-million salary, “bullying” behavior and “mediocre” recent performance of co-founder Bill Gross.

Word of the investigation follows a series of setbacks for Pimco, including the abrupt departure of Gross’ heir apparent, Mohamed El-Erian, reports of clashes between the two, and an outflow of more than $65 billion in funds from Gross’ signature Total Return Fund as disappointed investors cashed out.

Pimco said it is cooperating with an examination into whether improper accounting for bond prices contributed to the early reported success of a retail exchange-traded fund set up to mirror the investment style of the Total Return Fund, whose clients were giant institutional investors.

The Total Return Fund is the world’s largest bond mutual fund, a staple of 401(k) and other retirement plans across the nation with $221.6 billion in assets at the end of August.

The $3.6-billion Total Return Fund ETF reported investment gains of 8.7 percent from March through August 2012, its first six months of existence. That compared with a gain of 5.2 percent for the Total Return Fund it emulated, which at the time was growing rapidly and exceeded $270 billion in assets.

The Newport Beach, California, company denied it had done anything wrong. A spokesman said they believe their “pricing procedures are entirely appropriate and in keeping with industry best practices.”