Maybe you just got a weird corrupt reference. Have you tried deleting the ore and marker and starting over? (I assume you have) Otherwise I have to assume that you are just doing something wrong. Are you SURE you are making the marker the linked ref of the ore? I can't think of what else it could be... :/
Possibly... I had posted a similar issue with my scripts not saving:
Allrighty. Im extremely confused. I got home a few minutes ago, turned on my computer, started up skyrim immediately to do some gaming... and used my mod (You know... cuz its awesome and everything) and guess what? Everything works... Perfectly in fact.
Now this confuses me... Since last night, when this issue has been happening, No matter what I did, couldnt get the script to update. Today, works fine. What confuses me, is I have done absolutely nothing since last night. The only difference is today, I did not have the CK up and running while I was playing.
So... uh... WTF?
I had stated that in my other topic. Today, upon returing to the CK and Skyrim. Everything works fine. Something must have either been severely glitched with my memory (RAM needed to be cleared?) or something else program/memory related. Dont know... Didn't do anything, everything works fine.
EDIT:
Just in case you're curious as to my scripting issue: http://www.gamesas.com/topic/1354223-my-scripts-dont-appear-to-be-saving/