Well, there's obviously a bug with it. I'll report it but wanted to post here. Apparently when you donate logs, the kind that you actually cut from the jungle, it moves ALL logs. This is what happened to me, I put one set of Creator Bundle logs in one of my Places. I then opened another couple of Bundles and was holding on to them. I then went and logged a bit and donated those logs. Well, now I can't take back the weightless logs that I wanted to keep to myself without taking all three stacks or leaving them behind.

Yep, there's already a couple petitions for this (#652 and #661).

I'm guessing this was unexpected, as most folks probably wouldn't go logging and/or mining while already carrying thousands of weightless logs and stones. That's my best guess, anyway. The 'transfer all' is probably set to look through your whole inventory for any instances of "logs" or "stones," and wasn't set up in the long-long-ago to differentiate between "backpack" and "lodge bag."