i had such a problem too.
But this was in the time of any new hybrid edonkey version.
I think i solved it with deleting a .dat file. Then move all partially files out of the download folder.
Starting the donkey and exit it after one or more searches.
After this you move all files back to temp dir and start it again.
This (i think) was the way to get it fixed on a edonkey version.
But you can give it a try and tell me.
(sorry, but i really dont know anymore which file to delete, but i think this file isn't present on amule so that shoulndt be a problem

)