News of Glory's undeclared payments broke in December 2014, when sources close to the situation confirmed to The World Game that Fairfax Media reports at the time of undisclosed agents' fees, private cars for players' use and free accommodation were true.
It was alleged that in the 2012-2013 financial year, 15 individual payments totalling $50,602 to football agents for transfers, contract negotiations and scouting were not accounted for in the club's annual A-League player contract register.
The sources also confirmed the reports of evidence of undeclared player agent fees relating to the 2011-2012 season when Glory reached the A-League grand final, where it lost 2-1 to Brisbane Roar at Suncorp Stadium.
The documents confirmed Glory had 18 cars on its books in season 2013-2014, at least half of which were believed to have been used as an incentive to recruit and retain players.
They were provided with vehicles for the duration of their time at the club but were not included in the salary cap.
Most cars were provided by private sponsors or rented and it is understood they were valued at about $20,000 each.
The practice was reportedly in place for accommodation allowances in 2012-2013.
Some players had the cost of their entire stay in Perth provided by the club but that was not included in the report, as required.
Some amendments were made for 2013-2014 to provide more transparency, with at least two foreign players listed as having their accommodation provided by the club for a combined sum of $48,000. Though at least one other accommodation deal was not reported that season.
FFA's statement stressed the show cause notice "does not allege that these payments resulted in the club exceeding the salary cap in the relevant years.
"The alleged breaches involve failure to disclose benefits to players relating to accommodation costs, car allowances and the payment of third party agents fees for the 2012-2013, 2013-2014, 2014-2015 A-League seasons."
FFA will send staff to Perth next week to continue the detailed audit of the club's affairs.
League leader Perth confirmed receipt of the show cause notice on Thursday afternoon but declared in a statement that: "The notice does NOT relate to ANY alleged breach of the club's Salary Cap in any season.
"Furthermore the notice does NOT allege that the club exceeded the cap in this or any Hyundai A-League season.
"The club has always operated within the Salary Cap for each and every Hyundai A-League season."
The A-League salary cap rules stipulate that all service agreements that include motor vehicles, accommodation not including relocation, sign-on fees, performance bonuses, airfares, health insurance and player agent fees, must be declared to the FFA.
Fairfax Media revealed that Glory shifted two of its highest earners, believed to be Michael Thwaite and Nebojsa Marinkovic, onto marquee contracts in order to meet the forecasted salary cap of $2.55 million for this season.
Glory contended that it has cooperated with FFA and will continue to do so in an attempt to resolve the matter during the next week.
The punishment for any offence found will vary depending on the severity, however if Perth is found to have not breached the salary cap, then a fine, likely to be in the tens of thousands, is the likely result.
If Glory is found to have breached the cap, then the punishment would be much more severe with a possible deduction of points.
Sydney FC as in December 2006 fined $129,000 and docked three competition points in the league's only salary cap scandal.
