I see you are running Linux. Do you have a swap partition? If so, this could be the cause. With RAM intensive calculations, MATLAB will sometimes force the system to use swap, which is very slow due to hard drive reads/writes and causes seemingly simple operations to take much longer than they should. How quickly/When this occurs will depend on how full your actual RAM is when you run a script. Next time a script is seeming to take a long time, check your RAM usage (and, why not, your processor usage as well).
If trying to return the value of a scalar is taking a long time, it could be because it is reading it out of swap, or else MATLAB is busy running a script in the background and you aren't realizing it. If you kill it, what script is interrupted? Is it a result of something you started?
There are any number of things that can cause slowdowns for MATLAB. If you want to try to resolve a specific situation, please provide some code (including error code) of something you think is taking far too long and had to kill.