Yeah... Also had the same issue my first play through.I have ALMOST completed the process for galgadorian and enhanced galgadorian using AE (man i love ME-interfaces and molecular assemblers). The only process that glitches for me is the auto-enchanting of books, because for some reason it doesnt understand how. I tried putting chests next to the thing and make it auto-pull and -eject, but the network still doesnt understand it. Its probably something to do with the metadata, but im not sure....
I think I added a fuzzy card to that crafting recipe but it still behaved weirdly. My recipe was configured to use enchanted books with enchant X. When I asked for the magical wood, if there was no enchanted books in the inventory, it would drop the books into the auto-enchanter, retrieve them with an import bus and would only craft magical wood with the books that actually had enchant X even with the fuzzy card. But, if I cancelled the task and reorder it, it would then work with the enchanted books that were on the ME system. Maybe the auto-crafting system has problems detecting the books being added to the system when the enchant is not the same....
This time, I am using LP auto-crafting(well...was, switching due to some LP limitations that are very annoying) and LP with fuzzy works perfectly for this. Since I manually updated all the mods, this might be fixed on AE or it works on LP because its a recent version.. Dunno. But, if AE still has this issue, I might keep this little piece of automation with LP....
Another way is using the emerald+book to get the, I believe, Flim Flam 1 enchant. This way, the auto-crafted books are always the same and ME can use them to craft magical wood.