Alright ..
I know that this is a huge necro-post, but I made an account here specifically for this thread.
I had the exact same problem (Tin always halting the AE auto-crafting), even when I unhooked all machines except storage, smelter and 1 interface.
Looking for a sollution to this exact problem Google pointed me to this thread (with nothing I hadn't tried yet, so no solution).
HOWEVER! Just as I alt-tabbed back to my game it suddenly hit me:
Storage Drawers.
They were staring right at me and I realised: I had them locked so they only take in what they are locked to.
I had them locked to IC2 tin.
What happened: Whenever I smelted tin, it got pulled into my storage drawers.
Appareantly Storage Drawers (when locked) convert ingots to the corresponding (locked) type.
So every TE Tin ingot expelled from my alloy smelter got through the ME system into the Storage Drawers where it was converted to IC2 tin ingots.
Once I unlocked the tin drawer and put in TE ingots the problem went away.
So:
Check if you have any IC2 tin ingots locked in storage, unlock and remove it, place/lock some TE tin ingots (or no lock at all) and done.
Hope this fixed your problem, too (and anyone else having this problem).