I cant say that it would be the shell for sure, since Ive never used it, but I looked it up befor responding to this.
The shell seems to be a re-write of most of the entire phones functions inorder to give it the animations and looks that it does.
If not that then it could be somekind of application that just pulls the phones native information such as the messages and ports them into the shell to re distribute the data where it is needed.
Again, I am not sure, but if that is the case, then I would deffenetly say that the shell would be the problem,
Somewhere along the lines it might be lagging or glitching the information causeing you message freezes.
I saw that that shell is a paid app, so I could understand why you might want to keep using it regaurdless.
You said youve already updated to 6.5, but there is a nice rebuild of the sprint rom for 6.5.3
heres a
link
It wouldnt hurt to see if this rom is better suited for your shell
If not, maybe any other rom might give you a better look with out your shell,
That shell looks like it has alot of Android style menus, and there is an energy rom that has alot of the same looks from what Ive seen
heres a
link to that
Of course if you dont want to flash a new rom, wich is understandable, you can always just try out MaxSense with is the foundation of that rom style.
heres a
link to that.
Im not sure what else to tell you as far as the shell goes, but this is all I can think of at the moment
cheers