The same thing is happening to me since upgrading to 9.6 SP1. I've seen in the 9.6 SP1 release notes that mini scan files should use .miniscn file extension now but the csvImport.exe utility creates .ims files. Haven't found any other documentation from LANDesk regarding the change or an update to the csvImport.exe utility. This was working great in 9.5 SP3.
Just to chime in ... if we take the files created by csvimport and change the extension and reprocess they work. So - not an issue with the content in our case - just that the scanner will not consume the old extension type! Of course we are just as stuck - unless we write a utility to take the .ims files that errored, rename, and place back in the scan folder - ugh!!!