If a multi-TIFF file is readable, then by default it is moved it to the directory you specified for identified images in the Configure image file source and destinations dialog, if one or more of the images in the files are not identified.
You can change this behavior by adding the MoveUnidentMTiff setting to the [Options] section of Eiglobal.ini.
0 (off – default – the program reverts to the default behavior described above)
1 (multi-TIFF files are moved to the directory you specify for unidentified images if none of the images they contain are identified)