Hi, thanks for posting.
This warning gets triggered automatically by the engine when either the
Max Number Of Processing Threads is set to 1, or
Allow Parallel Execution is set to False. The warning will not be shown unless the solution is recorded to have at least one test with an execution time of greater than 25 seconds. The warning will also take into account grid nodes, so it will only show up if you are not using distributed processing. The comparison is fairly simple and well contained. To my knowledge, there is no way for it to malfunction.
The inheritance system in NCrunch's configuration can sometimes make it complicated to see which configuration settings are actually being applied. Check the Configuration window for the settings involved to make sure that they aren't set to something unexpected. It's possible for these settings to be overridden by engine modes and they can also be declared at solution and global level.