When USE="-dv", libdv is still autodetected by the configure script, introducing a binary dependency that doesn't have it's RDEPEND counterpart. That makes the package subject to breakage by "emerge depclean". Simple patch follows.
Created attachment 49410 [details, diff] mjpegtools-1.6.2-r3--use_dv_fix.patch
patch applied, thanks for your report and effort.