Summary: When 1000 or more Tomes of Secrets are in your inventory, it is impossible to craft gems. The "Required Materials" area of the crafting window reads "*/3" (in the case of crafting Perfect Squares from Flawless Squares) tomes available. Reducing the number of ToS in inventory to 999 or fewer enables gem crafting once again.
Steps to reproduce: Place either a single stack of Tomes of Secrets with the maximum per-stack quantity of 1000 or multiple stacks with a total quantity of 1000 or more in inventory. Try crafting gems. Note that number of tomes in stash does not affect behavior.
Expected behavior: Can craft gems, assuming one has the requisite number of gems on hand.
Observed behavior: Crafting does not work, irrespective of number of gems in inventory. Tomes available section reads */x in red resource-not-available font, where x is the number of tomes required to craft a particular gem; e.g. 9 for Perfect Square, 20 for Radiant Star, etc.
Notes: This bug makes crafting ever-better gems difficult. For example, a total of 1631 Tomes of Secrets are required to convert 729 Flawless Square gems into a single Radiant Star. The only way to perform the crafting is to have at least two stacks of tomes with 999 or fewer in each stack. One stack is in inventory, the other starts in the stash. Further compounding the problem is that if one has a full 1000-stack of tomes, the only way to reduce it to the necessary 999 or fewer is to sell a single tome on the Auction House. This bug can be worked around, but is also an unnecessary complication.
Speculation: There only appears to be enough room in the "Required Materials" section of the Jeweler's crafting window to display a 3-character number for tomes available. I have not tried crafting at the Blacksmith to see if the same behavior exists. Nor have I tried crafting lesser gems that require other tomes or when having 1000 or more gems in inventory. The same bug might surface in these cases as well.