I played some more and saw a bit more pattern.
Only units ordered to auto hunt and auto explore are affected.
Not other ordered units.
I have a suspicion, but I can be wrong because I'm no C++ programmer. Here goes...
I suspect that Koshling gave units that explore or hunt the "instinctive" need to join stack for safety. So I wonder if you exclude that code from human players and maybe that "bug" will go away?
I can be wrong because Koshling is your Padawan, and I'm barely a code-sensitive person .
I pinned down the tendency of automated hunters to return to cities after a while (it wasn't a new thing - it's an old bug), and it may well be the same for explorers (I'll check). The fix for hunters I pushed to SVN July 15th, but it looks like I only pushed it to C2C. I'll check if explorers have the same isue (and fix if so) and push to AND SVN as well today. Basically the bug is that some automations (hunting certainly) had code that basically said 'if were at war go join an attack stack since hunting alone doesn't make sense in wartime'. This clause should only apply to the AI, but was wrongly being applied to automated human units also.
HOWEVER, this doesn't explain 'getting stuck on a task' necessarily (though you might be mistaking what is actually happening for that), it just explains them coming home to join stacks (deliberately). Might well look like the same thing though.
Edit - ok, pushed to SVN (along with the resulting DLL). Also pushed a small Python change to fix the sensors promotion that was crashing someone a few days ago (the carsh aspect I had already pushed a fix for, but this now fixes the intended functionality too). Revision 514