Perhaps Transmute charges were bugged the first couple of weeks, but as it stands now after the adjustments, Transmutation specialization is a tragedy - a complete waste of points.
One or maybe two transmutes a day, realistically? I can farm 100x more awakened elements with fledgling miner or herbalist alts with no gear in the time it takes for a fully-specced Transmute specialist to gain extra awakened elements. There’s no point to this specialization right now. Besides the first-time craft bonuses, no one is going to want to transmute Decay or Order into elements. Order is by far the most expensive and rare awakened element at the moment, and the biggest driving force in causing sophic weapon enchants to be at the price they are.
Please ,either allow more transmutes per day (like 4 or 5) for fully-invested Transmutation specialists to fish for multicraft or resourcefulness procs when side-grading elements, or give Alchemists a recipe or ability to “Transmute: Elements to Order” or “Elements to Decay” (perhaps a Decayology synergy).
To anyone else reading who might be taking alts into Alchemy, avoid the Transmutation specialization unless this is addressed. Go for something more useful, like potions of phials, or anything else under Alchemical Theory.