I can't really say that I knew WHY it is like this. I can only go on what I've read so far, which was I read in the Ubuntu Forum that I posted which states that Matlab (by default) relies on a "control terminal" to be open for it for it to run. I don't know if this is the exact reason for it, but it would seem to make sense.
Anyway, when you run it with the tag "-desktop" it must go into some other mode that doesn't rely on a "control terminal". There are many reasons for starting Matlab with different tags. I have to run Matlab with the "-glnx86" tag because Mathworks has yet to make a 64-bit Student version (the tech guy said something about them not thinking students would be running 64-bit systems, either that's not the entire truth or they don't really know students too well!). Without that tag, Matlab will try to launch 64-bit Matlab and won't work because I simply don't have 64-bit Matlab installed.
If you try to type just "matlab" in a Run Command, it will look for a "control terminal", since it is not there, it won't work. When you add the tag "-desktop" it will not require that the terminal be open. It just starts in a different mode, thats all.
The "control terminal" method is probably set to default because that is the only way that you will get any feedback from Matlab if it has to close. That's my take on it anyway. I would not say that it is a "bug", that's for sure.