We have several dozen people who have been using the prusa i3 mk2 profile in S3D for almost a year now. A lot of their work involves manipulating the fan cooling settings, and they have not encountered any of the issues that you mentioned. I am pretty confident the stock profile in S3D works correctly, but as others have said, it is definitely possible to make changes to the profile that can cause incorrect commands to get inserted.
Is there a reason you have not attached your profile to this thread as other have suggested? It will be very easy to see what changes you made once you post your profile. Otherwise this seems like a waste of time speculating without any data or proof!