I reported something similar already ...
https://forums.elementalgame.com/393806
... and I'm very glad, that I'm not just imagining things. *grins*
But concerning your post, NTJedi. I think that it is not just a middle or late game problem. My assumption is, that it happens all the time and that you just don't see those shards as they are in areas of the map you just have not explored so far. This would also coincide with my observation of a positive correlation between the number of new shards I observe (everything from zero to three so far) and the percentage of the map I have explored.
Concerning the relationship between reloading and shrine graphics I haven't had a problem so far. Although the air shrine graphic has been missing since the beginning. I never have seen of those displayed correctly. Air, earth and fire work fine for me.
Rabenhoff