I've always had a spot of cyano bacteria in my tank in the corner by the rock work never really spread it was always there I would use chem clean and it would go away for a little bit and come back but since I stopped doing water changes it slowly went away and hasn't come back and it's been almost 5 months.
Sounds like your water may have been the source of the issue. Were you using your own RO/DI water?, Tap water?, well water?, store bought water, etc?
The contaminates may have increased the desired beneficial components the cyano needed to thrive in that less circulated area. Think I read silicates from the water can lead to small outbreaks. So may not have been the water changes or your process, but rather the water source of the changes.
I believe water changes are good overall. They make sense. Remove waste, pre-introduce new elements, calcium, magnesium, etc into the water and just freshen up things.