For Checkpoint versions 2014.11.28.xxxx some users are having a problem with primitives "disappearing" from the Landmarks tab even though they can be seen in the 3D window. This has been identified as a bug and will be fixed in the next update.
In the meantime, you can edit the .ckpt file yourself to fix the problem. To do this:
1) Make sure the specimen is *not* loaded in Checkpoint.
2) Find the .ckpt file associated with the specimen that is having the problem, right click on it and selectOpen With... | Notepad. This should open MS Notepad and list all your landmark information.
3) At the bottom of the file is a section called [Sorted Primitives] and you should see a two lines for each primitive. The curves for example look like:
-1 -1 50 -1 -1 -1 51 52 -1
4) The "-1" entries are the problem. Change those two lines to the following single line (which will cause Checkpoint to regenerate the order when it loads the specimen next time):
5) Save and close the file in Notepad.
6) Re-open the specimen in Checkpoint and verify the proper order of your curves.
We will take a closer look at this issue and try to ensure that it does not happen in future versions. We apologize for any inconveniences this has caused and appreciate your patience while we repair problem.