Mindscape used a lot of different protections throughout the 80's, and most all of them were difficult to copy with serial nibblers. I have run across titles protected with their early efforts that use gap signatures, V-MAX, as well as their last protection that is detailed here.
The protection on the disks released from 1988 and later is based on "bad GCR", or more than 3 '0' bits in a row. The way the protection works is that it reads in a sector (from track 1, sector 1 in this case) and checks that 3 bytes between two $AA anchor bytes are different in successive reads, and the following bytes are $D4 $EE. This protection is sometimes difficult to detect because when copied, it will simply read a semi-random byte that may or may not be a good GCR byte in between the $AA anchors, as well as sometimes the framing is lost on the $AA, corrupting the $D4. If it's read as a bad byte we can detect it and write out a bad byte to replace it when reimaging, but if it happens to read as a valid byte, we never know it's there unless we disassemble the code.
This protection can be reproduced with MNIB, and the emulators with bad GCR support with load the disks converted to G64 with the "-f" option.