I've read from a few places training manuals are not working, yes.
Rather than cry about your efforts going to waste, consider the big picture. A pointless system is being removed from the game. Training manuals were less of a reward and more of a punishment if you lacked them. Advancing levels of a craft opens up new recipes and makes older ones easier, if you don't think thats a reward...
http://hahnemannkiaawaz.com/wp-conte...ying-baby3.jpg
You're playing an MMO during what at best can be termed its "formative year," or at worse "premium beta." Its why you're not being charged right now. If you didn't expect shit to change, I'll kindly ask you to continue crying.
A) It has already been stated multiple times by SE that guild marks are on their way out and that B) players WILL be compensated for the guild marks they spent. When and how said compensation will be implemented remains to be seen.
