There does seem to be an issue with the current version that causes the bot to be unable to re-enter crafting after it fails a synth under certain conditions. I have already asked Cooleko about it and since he is totally reworking the crafter, fixing this issue isn't high on the priority list.
If you are doing anything that needs the use of creative this can be a pain in the butt as it is harder to maintain success when the bot always want to use creative.
However, if you are working on achievements like me or don't care about reducing your xp gain/synth you can get around the bug by equipping a bunch of abilities that aid against failure and reduce durability loss (fulfillment, makers muse, creative urge, aspect balance, and tender touch is my loadout) and then set the bot to no careful/no wait. Under this setup you should never fail anything and the program will never get confused.