It also may be the Baqua. When we were using it we had problems, and asked the dealer for advice.
He asked us if our water smelled musty, or like dirty socks. Is that the kind of smell you have?
He said it's a relatively common complaint among Baqua users, and recommended we stop using the waterline control and switch to Spa Perfect instead.
We did try it (It was even more expensive than Baqua's stuff) and it didn't help so we dumped the Baqua.
Ask your Baqua supplier if they get those type of complaints, and what they recommend.
If you do switch, you're going to have to get rid of as much Baqua water as possible, including the gallon or so that may remain in your plumbing after you drain.
I had to put a wet vac on the jets to get all of ours out.
I also did the swirl away treatment prior to draining.