Daniel,
It looks like it is reading a V3 file, and the file size from the attributes is bigger than how much data it read from the file. This is probably due to some sort of disk data corruption.
At line 722 of /usr/share/BackupPC/lib/BackupPC/Lib.pm there is this code:
$md5->add(substr($$dataRef, $seekPosn, 131072));
You could try replacing that with this:
$md5->add(substr($$dataRef, $seekPosn, 131072)) if ( length($$dataRef) >= $seekPosn );
Craig