A number of the gems specific to Solhaven and River's Rest cannot be placed in alchemy jars, I believe because they weigh more than two pounds. This is frustrating to us stockpilers. If it isn't a deliberate attempt to prevent stockpiling, is there a chance that either jars could be made capable of holding larger items (if that's the problem) or the gems could be made smaller? Gems that won't fit include but aren't limited to:

a split-back pink conch shell
a giant paper nautilus shell
a polished red abalone shell
a polished silver abalone shell
a polished green abalone shell
a dark brown triton shell
a golden triton shell
a piece of flower coral
a piece of cat's-paw coral
a piece of blue ridge coral
an empress's crown shell
an emperor's crown shell
a black helmet shell
a king helmet shell
a queen helmet shell
a yellow helmet shell

The majority of shells fit just fine, including many similar to the non-fitting ones (black-spined conch shells fit, for example, as do striated abalone shells).

>yeah all shells are incompatable with the alchemy jars. It's always been like that.

This isn't actually true; the majority of shells work just fine in alchemy jars:

In a deep chest:
a long-necked glass jar containing checkered chiton shells
a long-necked glass jar containing polished black tegula shells
a long-necked glass jar containing fluted limpet shells
a long-necked glass jar containing angulate wentletrap shells
a long-necked glass jar containing white gryphon's wing shells
a long-necked glass jar containing large chipped clam shells
a long-necked glass jar containing amethyst clam shells
a long-necked cyan glass jar containing beige clam shells
a long-necked glass jar containing checkered chiton shells
a long-necked glass jar containing sundial shells
a long-necked glass jar containing snake-head cowrie shells
a long-necked glass jar containing pink-banded coquina shells
a long-necked purple glass jar containing three-lined nassa shells
a long-necked black glass jar containing black-spined conch shells
a long-necked glass jar containing opaque spiral shells
a long-necked glass jar containing candystick tellin shells
a long-necked brown glass jar containing Solhaven Bay scallop shells
a long-necked glass jar containing striated abalone shells
a long-necked dark glass jar containing polished batwing chiton shells
a long-necked glass jar containing purple-cap cowrie shells
a long-necked glass jar containing golden cowrie shells
a long-necked glass jar containing lavender nassa shells
a long-necked glass jar containing spiny siren's-comb shells
a long-necked glass jar containing translucent golden spiral shells
a long-necked blue glass jar containing leopard cowrie shells
a long-necked glass jar containing blue-banded coquina shells
a long-necked glass jar containing pink clam shells
a long-necked glass jar containing white clam shells
a long-necked glass jar containing tiger-striped nautilus shells
a long-necked grey glass jar containing sparkling silvery conch shells
a long-necked glass jar containing tiger cowrie shells
a long-necked glass jar containing egg cowrie shells
a long-necked glass jar containing snow cowrie shells
a long-necked glass jar containing silvery clam shells
a long-necked white glass jar containing dovesnail shells
a long-necked glass jar containing large moonsnail shells

So if all of them used to not work, it should be even easier to fix the few lingering non-fitting ones.

Any gem/shell with a script won't work either. I don't know if that's the issue with the shells, but a fair number of rift gems won't fit in jars for that reason: Eye-of-Koar emeralds, aster opals, faceted black diamonds, oblivion quartz, shadowglass orbs, firemote orbs, and the highest end faceted thunderstones. All are scripted and none will fit in jars.

Kerl