MJ on Mini
I have similar issues on my mini.
Not a problem with the computer. You can be running nothing (except the normal bg processes) and still have issues. Ours was on my wife's Windows Vista laptop before I moved it - kind of hard to have a phone plugged into a computer that is constantly moved around.
QOS does help. Just go into your router and look for it - I found mine under "gaming" on my Linksys.
I cannot remember the ports at present, one was 80, which is http - I didn't add that one! Two others I added. I saw some immediate improvement.
Still, it can "clip" and be "choppy" at times. This can depend on both your ISP and MJ's provider. And traffic on each. Nothing you can do about the latter or the rest of the internet.
You should, by their admission, get good results on a slow DSL line (128k up/768k down).
Also, you can "renice" the MJ process(es) under Terminal, but I haven't seen where it did much. If you aren't running anything else, it doesn't need it. If you are running something else, it may help - probably not much.
At any rate, if you read "true" reviews, not the MJ propaganda, you will find that it will not match VOIP from providers like your local cable company or Vonage. You get what you pay for, usually.
And if you look around, you will find that some have turned to buying a system that is solely used for the MJ, with custom setups (read: no frills, stripped down OS). There is a guy who sells HP servers for such use! But the $$$ is a little much for me.