Short Explanation. The different values represent differences in scaling LINKMAP's representation of the likelihood value. If you run the post-processor program which computes odds, the discrepancies will disappear.
Long Explanation. Because LINKAGE computes with very small numbers, these numbers must be scaled to avoid underflow. Any (log) likelihood values that are printed out by any of the LINKAGE programs are actually scaled by some amount that depends on the structure of the input pedigree(s). Various scaling rules can be used. In LINKAGE 5.1, the programs LODSCORE, ILINK, and MLINK all use the same scaling rules, while LINKMAP uses different scaling rules. We could find no internal or external documentation to explain this difference. The difference arises only for some pedigrees that have loops.
To increase the amount of code that the four programs can share in our versions, we have decided to make our LINKMAP use the same scaling rules as the other three programs.
If you would like details on how to modify our LINKMAP to make it consistent with the old LINKMAP contact schaffer@cs.rice.edu. The necessary editing is simple, but you would have to edit the code each time you switch between LINKMAP and one of the other three programs.