Hi There
Sorry you are having problems. There isn't a lot more that can be added to the error message itself, all it is doing is comparing the base morph vertices exported from the 3d package against the Unity vertices and trying to find matches using different coord systems, and calculating any scaling Unity or the FBX exporter/importer has added, if it cant find a match then it will report a failure.

There is a section on the morph page that explains why mapping failures happen and ways to avoid them, and the reasons there have been why every mapping has failed when the user has finally found what was up. If you continue to have problems you can email me a test case of the maya file, the fbx and mor file and I can investigate further.

Maya like max seems to have various kinds of pivots it uses, Max has object pivots and working pivots and I believe Maya has the same. There is hardly ever an issue with objects made in Maya and then duplicated, altered and used as blendshapes, all the problem morphs from Maya seem to come when people are using people or objects purchased from other sites etc and it has been found that one of the pivot types has been relocated or transformed in some way. I am not a Maya coder, I managed to learn enough to get the exporter working but currently I know very little of the internal workings of the package to know where to locate the pivot data and automatically adjust it, I hope to do this in the future though.

The fact that an older version of MegaFiers has loaded a mor file a couple of times and then found mapping issues a third time is very odd. There has been no change from the mor file loading and mapping code since it was released not sure why an older version would show that and not a newer version, maybe the base mesh got altered in some way before loading the mor file.

If you would like to send me the files to look at then that is fine sometimes I can see what the problem is other times its very hard to track down. But the main things to check for as listed on the morph page are pivots on the main or target objects having been changed. Or the first frame of an animated blendshape not matching the fbx mesh, ie T-Pose in the fbx, idle stance as frame 0 of the blendshape animation. Or a modifier applied after the blendshapes in Maya such as a smoothing system, this will change to the vertex count, positions etc and make mapping impossible.
Chris