You are right, the Beta version amp(integrated?) could very easily be the problem. Everything is SET/audio is a tradeoff and there is no free lunch. It's easy to get one factor right, but all of them take skill, experience, and/or money.
The designers of your amp may be focusing on subterranean bass at the expense of midrange magic or highs. Or, they simply may not have the circuit fine-tuned yet. There is a reason why it's a "Beta", afterall.
I just started to get into high-eff speakers and SET's last year. Believe it or not, in a massive town like Los Angeles County(265 sq. miles), there are only 2 or 3 shops that carry single-ended gear. There is no way to get any idea what it's all about.
Regardless, whenever you get into something new, the first few tries are more about finding out what you don't like than the opposite(unless you get horribly lucky).
As a result, I decided to buy well known, well received, amps of mature designs (nothing new), that I could easily resell for breakeven after getting a good sense of what they have to offer. There just no substitute for 1st hand, personal, experience in your own system. I am now on my 4th this year. Every single one has had something great about them. But, then the others have been just as good in their own way.
Do not get shackled to one amp that may not have any resale value, there are a plethora of great companies making superbly affordable SET gear these days. Especially, in your ($2k-3k)price range if a used Cary SEi was possible - ASL, Welborne Labs, Almarro, Sophia Electric, Eastern Minimax, Opera Consonance, DiyHiFi, Decware, Bottlehead, etc.
All of those make first rate amps that have a proven performance record are easily resold along with keeping their value.
Perhaps you should try something different if you can get your money back.
