I'm at the end of my rope with it, honestly. Just ask the ALiVE devs, they've heard me bitch enough about it lol (though one bug was fixed by HH in the process so I guess something good came out of it :) ).
I honestly have no idea what to do. Every few seconds, even off map, it stutters on these maps. I've done everything I can possibly think of on my end to resolve it. A couple weeks ago I went back through over a year's worth of CBA releases thinking that might be the culprit and it was still there for all versions, on all maps with the stutter.
I know it's not ALiVE related either, because I have the same problems playing the Chernarus version of the mission Pilgrimage (the Altis version has no stutter! Lol). Though I do believe ALiVE calls whatever function that can make the stutter happen. For instance, on my Sangin mission with ALiVE, oddly, I can make the stutter stop by removing all CS modules (WTF?). But on other maps such as Diyala, the presence of CS makes no difference. Makes me think some engine function is borked in some way, but surly I wouldn't be the only one with problems.
I've pretty much resigned myself at this point to just not use those maps and hold out hope someone smarter than me will see it too and publicly ask about it and solve it. I saw one post about this on the "DayZero" workshop thread dated May 28th but he had no replies. :(