Welcome to the forum, Teegr. I too have had a problem in the past with this. I am not completely aware of all the reasons for it but I have learned that it is related to hitting the ph markers correctly first of all which affects the cheese's texture. There are a lot of other variables related to it as well, but just from an amateur's experience, since I have started measuring ph, my cheeses have all melted much better. By the way they also change as they age; are you letting them age?
I am sure someone will give you a more thorough answer than this but I just wanted to give you the general answer first. You can search the forum also because there have been several discussions on this. Click here
for one of those threads that has two off site links on melting and stretching of cheese. Here
is one from the library too. Good luck.