If you have a Gem in the first free slot in your inventory and you then buy a diamond/emerald through a shop plugin, or you get them as a vote reward. It will add to the stack of gems rather then making a separate stack of plain diamonds/emeralds.
This bug is very damaging as the % drop chance is so low for them normally.

We'll look into that. Thanks for the report.

Reproduced. However normally you can't stack lore items unless they are exact, Fixing this unfortunately is not possible at the moment, considering it involves an issue with craftbukkit's methods of adding items to the inventory.

Fixed in 1.4.5R1.0. and build 358