X99M Extreme4 4pin fan header no 3pin fan control

Four pin fan headers are typically of two types on mother boards, although IMO they really should not be configured that way.

True four pin PWM speed controlled fan headers, as the CPU FAN1 header always is on any modern mother board, will ONLY control the speed of four pin PWM fans.

That is not a new standard, and every Intel stock CPU cooler has a four pin PWM controlled fan. I insist upon four pin PWM fans on my CPU coolers, the automatic speed change with temperature is a great and basic feature that I would not do without.

All three pin fans use voltage control to change their speeds. As said above, you cannot expect a three pin voltage speed controlled fan to have its speed controlled by a four pin PWM header.

ASRock usually also provides PWM speed control on the four pin Chassis 1 fan header. Many boards may use voltage control on what appears to be a four pin PWM header, which causes confusion for some users when their three pin fans can have their speed controlled on these four pin fan headers. These fake PWM fan headers are a true disappointment to users like myself, that find their PWM fans will not operate over the full RPM range that PWM provides.

You did not specify which fan headers you are using for the two, three pin chassis fans, but clearly one of the headers you are using is a true four pin PWM controlled header.

The board does not have any problem with its fan headers. I'm sorry you are disappointed with your three pin fan's operation on a four pin PWM fan header, but nothing can be done about that. You are simply using a fan (three pin) on a fan header (four pin PWM speed controlled) that is not compatible with three pin fans.

Your board only has one three pin fan header that can control the speed of a three pin fan. It might be possible to use a one to two fan splitter cable, to power and control both fans from the single three pin fan header. The power usage of the fans will determine if that would work. The label on the fan's center hub normally states the current in Amps used by the fan.

Personally, I wish three pin fans would be phased out, and all fans would be four pin PWM speed controlled.

Regarding the board's warranty, where did you see it stated that the board has a three year warranty?

What newegg offers as waranty is binding, so you are covered by them for 3 years vs the ASRock standard 1 year. I don't see what is confusing, if anything it is incentive to buy from them which is likely exactly why they offer a 3 year warranty. Now if you purchased from elsewhere and they adhere to the standard 1 year warranty and are complaining that ASRock offers less than newegg that isn't the fault of the manufacturer, that is incentivized marketing on the part of newegg. Manufacturers often have extended warranty plans for distributors, it costs the distributor an additional fee and in all likelihood that is the case with newegg as they are a very large distributor.