Description: Ubuntu 14.04.2 LTS
Release: 14.04, running on AWS virtual server.

Minecraft Version build using BuildTools, downloaded on Oct 2.
Most recent build, Nov 30, 2:43pm.
Version: This server is running CraftBukkit version git-Spigot-f950f8e-eb6c1bf (MC: 1.11) (Implementing API version 1.11-R0.1-SNAPSHOT)

Normal world, generated with my plugins installed (mostly interactive), currently all plugins disabled. ("/plugins" result is "Plugins (0):").

Crafting Table is placed in a Village house, against the wall, between two double-chests. Nothing else of any note around or near the table.

One step further. I've been playing in survival mode, and have managed to collect wood and leather. I just went to make myself some Frames, and when I place them on the crafting table, they show the resulting object for an instant, and then it disappears. However, if I "give" (command) myself new sticks and leather, it works just fine.

The stack of leather and sticks are in a chest right next to my spawn location, with a crafting table behind you. http://mc.goal-time.com – if anyone wants to see the issue. Don't know if it would help to troubleshoot, but the command "/gtdebughanditem" should tell you what it is.

The "put it in my hand" trick does not fix this one. I am definitely confused.

I restarted the server, and had been using my plugins, and started having problems again. I've since disabled them, except a simple "give me details about the item in my hand" plugin.

I have two stacks of logs, one is a count of 57, and one is a count of 3. They will not stack. If I stack them in a chest, they will, but when I reopen the chest, they are unstacked. The ... UGH. Okay, I was going to give you the server address, to try to see what is happening... but the issue is resolved now.

Same problem appearing with Coal. No clue why. Move them from box to box, try both on crafting table, and one stack will form blocks, and the other will not. Place them in the toolbar, and select one (active hand), then the other, and now they will stack and create items!

Do items get "changed" somehow when they are placed in the active hand?

I am floored by this. Not upset at all – still not sure if something my plugin is doing is causing this, or whether it's a fluke. I'd take any theories at all, and try to reproduce them.

Thanks!
-Lee

Went as far as to simulate 150ms of latency and could still not reproduce this issue with dark oak wood planks to build stairs

I disabled every plugin, and was still having the problem, but thanks for trying to reproduce it. It appears that anything with multiple recipes might be causing the problem. Have restarted the server multiple times, and no luck. I'll consider regenerating the world completely...

I tried to reproduce this and was unable to. Oak stairs, sticks, fence, fence post works.
You should try to disable not only your plugins but all plugins.

Ran the version command, and realized I was still out of date. I went ahead and re-ran BuildTools, and got the new version set up. Still having the same problem.