2-3 weeks ago, while playing with a friend, he said "I have x Rekuta", which prompted me to look at how many I have. The total was something like 583.
Now, I harvest every Rune node I find, so since then I had found quite a few, including at least one node that gave me 5 Rekuta, and a total of ten other Runes (so 5, 5, 5). I would say I had at least 600, but possibly as many as 620.

So I decided last night to unlock the remaining Enchant Achievements on my second character, who I've now got doing writs, and I thought I'd use Rekuta since I had around 600 of them, and I could then use them to level up other toons' Enchanting while I was at it.
At the crafting table I found I had only 400 Rekuta. So at least 200 have disappeared.

Now, before anyone posts anything like "but maybe you did x and you don't remember", I have four max level characters who have all had enchanted gear for some time; any glyphs I make for them are usually using Kuta anyway. And I rarely make glyphs for the lowbies, since what would the point be, they'd outlevel them pretty quickly. Even so, if I had, that would have used a maximum of maybe 40.
Neither have I crafted 200 glyphs recently - because a) I would remember that, and b) I don't have the bank space to store 200 glyphs.
And, for the record, I have not listed Rekuta for sale on a guild trader, ever.

On mentioning this to another friend she said she once had 10 dreugh wax disappear. She'd gotten them out to give to someone who didn't need them, but when she went to stow them they were gone.
And that starts me wondering, since the craft bag is largely out-of-sight-out-of-mind and most of us are probably only aware of the current total of gold mats at any given time, how many other mats are going missing without us noticing?