Craig (and anyone else who always leaves their starter out at room temp), do you find that leaving the starter out produces a less acidic starter? Approximately what ratio of starter to flour and water do you use? I'm assuming it's not 1:1:1, or the starter would become very acidic very quickly, right?
Probably - but because you feed (and dilute the acidity) more often when it's at room temp. I do the feeding by sight. I don't measure anything My normal feeding routine is to add some water - maybe 50% of the starter volume, mix it up, dump half out, and add enough flour to reach a thick batter-like consistency. That's it.
Your problem really surprises me. I've never had anything like it when using such small quantities of starter.
If I had to guess, I'd say it enzyme related more so than acid. If it was acid breakdown, surely you would have a strongly detectable acid bite in the dough.