I've had many problems with the assimilate program, as I know for a fact, this is a big problem people have. I know it is not my xsi file, as I am testing assimilate out, using one of the jk3 xsi files, which was recently released. The error I get, says that bones, such as ltarsal and rtarsal are not found. Then it has error code 1. I'm not sure, but r the ltarsal and rtarsal from jk2 or something. Well, if anyone can help me with this. My directories are working as far as I know.
Just to be sure check the xsi file and look for those bones... Probably you have deleted them or have done something to them you shouldn't have done...