Another related upstream bug has been fixed in SVN trunk: http://savannah.nongnu.org/bugs/?29766 "Path finding method eats CPU futilely when there is not possible path"
If I understand correctly, the pathfinder itself was not changed there, but the higher-level code was changed to retry fewer times if it doesn't find a path right away. This change is not in the boswars-2.6 branch. It is likely to be released in Bos Wars 2.7. I had some plans for caching the results from the pathfinder: http://savannah.nongnu.org/patch/?7141 "Speed up pathfinder by caching islands" but it now seems such a cache would require also hooking all the code that moves units, so I'd rather do that only if the current fix doesn't suffice.
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