So I was inspired by an article by Takashi Amano about using lighter substrate in the foreground and this weekend I pushed all my dark stuff and soil to the back of the tank, replacing the foreground with lighter gravel. Lo and behold, a few nasty bubbles and I've lost all my kribs and a neon.
Guess this is the anaerobic pockets people have mentioned. Never though it could be quite so bad but really awful situation. What did seem to help, besides the quick and frequent water changes was putting an airstone in to bubble away. It could have been a lot worse but guess I wanted to leave this as a word of warning for people.