IMHO:
Er... regarding the AE crafting issues, I can't find it ATM, but I seem to recall that AlgorithmX2 had a message about the most recent 1.6.4 versions of AE.
I believe that it came up at about the same time as he added Spatial storage. The quote I remember is: " (something to do with crafting) ... if you're okay with smacking the network every so often to reboot it (or words to this effect)." So, he knows about the crafting hang, at least, but didn't actually fix it.
Tentative conclusion: not a bug, per se, but a "feature". Or an "ascended glitch".