The latest claim relates to the current season and a failure to disclose reportable benefits and payments in excess of AU$100,000.
FFA announced on Friday that Glory - currently third in the A-League - would be fined and disqualified from the 2014-15 play-off series after being deemed to have systematically breached the salary cap in each of the last three campaigns.
Perth were set to seek an injunction against their exclusion in the Supreme Court, but, according to a club statement released on Monday, that action was suspended "in the spirit of the game, to allow the FFA appeal process to be exhausted".
However, Glory - who were also handed a fine of AU$269,000 - are yet to lodge their appeal, despite releasing a statement to the contrary on Wednesday.
The club stated their case would be heard later in the day, but the FFA described those claims as "erroneous".
"The Disciplinary Committee will hear Perth Glory’s application that the board of FFA had no power to impose sanctions on the club for breaches of the salary cap," read a statement from the governing body. "The committee will not be hearing an appeal against the FFA's salary cap determination and associated penalties, as claimed by Perth Glory in its statement.
"For the record, Perth Glory has not lodged an appeal against the FFA determination, which excludes Perth Glory from the Hyundai A-League Finals Series and imposes a fine of 269,000 AUD."
