Visual studio/Monodevelop causing warning "The reference script on this behavior is missing!"?

I have ran into a problem when editing scripts during play mode and having them recompile (while still playing). It seems that if I open up my unity project and do "sync monodevelop project" as I usually do to open visual studio (this problem happens with monodevelop too), and edit a script while in play mode, after it recompiles it will give me a "The reference script on this behavior is missing!" warning (clicking the warning gives no indication as to what script is missing). However, If I keep this visual studio solution open, go to unity file tab and click "Open Project.." and reopen the same project and do the whole script editing process again, this time I do not get the reference script warning.

Does this happen to anyone else?
Anyone know why this happens and how to fix it?

Thank you for any help!

For now I guess I will just have to open the visual studio solution before opening unity.