Are you sure this isn’t Mission Planner limiting the maximum to 2000 when you are changing the parameter? The parameter definition says the valid range is 20-2000 as seen here: https://github.com/ArduPilot/ardupilot/blob/Copter-3.5/libraries/AC_WPNav/AC_WPNav.cpp#L45. Perhaps Mission Planner is changing your 3000 to 2000 upon loading to respect the defined maximum? I honestly don’t remember if MP does that. If you refresh the parameters, see if WPNAV_LOIT_SPEED was set as 2000 instead of 3000 by Mission Planner.
Yes, I already had the idea that the MP resets the 3000 to 2000. However, this is not the case. I loaded the parameters from the copter the next day and there was still 3000 as maximum.
The EKF has a speed limit that appears to be related to optical flow. If you’re using optical flow, which I’m guessing you’re not at 60mph, it appears EK2_MAX_FLOW is a factor. If not using optical flow, it looks like the hard coded limit would become 400,000cm/s. I’m probably reading something wrong that @Leonardthall would know far better.