When NO Thaumic Speedup installed, information about stack aspects right, not depending on stack size:

When Thaumic Speedup there, itemstack have different aspects when amount != 1:

Its not only JEI or visual bug. When throwing items into crucible, if item entity amount not equal 1, its used wrong aspects.

There is i throw 2 Silverwood log in crucible, and it wont melt at all:
https://i.imgur.com/zu9mzJb.gif