Hey there,
yesterday is started collecting my missing skyshards from Stonefalls. My Journal told me about 6 missing shards. I located three of them without problems, but the other three (all of them [more or less] underground: Mephalas Lair, Emberflint Mine and Crow's Nest) were marked as "not found" in the Journal. I am quite sure I already picked these three up and I was not able to locate them. However, there were no non-glowing shards on the ground like the already-found shards, for example aboveground. Dunno if its relevant, but I collected those shards while playing in a group. I also tried relogging, but it did not help.
So long story short: Are there known issues with the recording of skyshards in the journal?
Greets!