Umm according to the picture you posted, both fans are running @ 1660rpm, the pump is running at 2367rpm. Which is exactly as it should be.
Since both fans come from a single source, with only 1 fan rpm actually read, I don't see how it's possible for one fan to be registered as spinning at any different speed from the other. Not unless you have some jacked up wiring and have each fan on separate headers and not attached through the pump wiring where they should be.
In the picture above, that supposed fan reading of 2800rpm is the pump rpm. The 750 odd under it is the case fans. And considering the bottom blue bar of cpu_fan is registering 0rpm, looks like you opted to use a sys_fan header to power the pump and a sys_fan header to power your other case fans.
Are you sure you wired up that AIO correctly? If you are positive all your wiring is placed where it's supposed to be, then Corsair Link has an issue. Pc's are not supposed to be able to function with 0rpm at cpu_fan header, the cpu will shut the pc down instantly if that really happens.