For some odd reason, with emistry script, it only checks the first mission in the list repeatable limit, so mission #2, #3, #4, etc, it doesn't get checked and will always let me do it unlimited times.
And when it does check (first mission), it goes per IP (even if there isnt a query for it). I first tried it with a GM character and completed a mission, then I tried to do the mission with a 'normal' character, and it said I've already done the mission.
For the eAthena script the only bug I noticed (so far) is that the "Only Once" setting lets characters do a mission twice instead of once.