Comment 5 for bug 685893

versions prior to 4.0 had a completely different algorithm. If there was one mistake in the move from 3.x to 4.x, it was that the 4.x algorithm *replaced* the 3.x algorithm instead of complementing it (with an option to choose which one to run).

the current GSoC project on Enblend is adding modularity to enable multiple seam placement algorithms under the same code base. It will bring a new challenge (how to determine which one of the multiple choices of seams is the best one?) that is already being thought of. Maybe it is also an opportunity to resurrect the old 3.x algorithm as one of the many options - one that is obviously superior in the cases that trigger this error.

as for the deliberate nature of the "questionable" behavior, have you tried to change the arbitrary threshold and see what happens? the changeset linked in comment #4 is very well documented. set overlap_threshold to 0 and run a test case against a recompiled version of enblend. please report interesting results here.