Just as xNiNELiVES reported last summer (http://www.magiclantern.fm/forum/index.php?topic=7388.msg62703#msg62703) there is a "ML/CROPMKS dir is not found" error any time Card warm-up is being used. The error is delivered right after warm up process is finished during start up. However, the CROPMKS directory and its files are there all the time and crop marks will be visible again by just turning Card warm-up off.
Nightly build from 2013-12-30 (I checked the change logs of newer nightly builds and found no comments related to crop marks) Canon 5DMKII ( Lexar x1000 64Gb ).
I am eager to provide any additional information if needed. Thank you!