As you describe, I entered the set %-screen, pushed the number up and down once or twice and settled back on 30% and hit ok. Not sure what else I could have done to avoid it.
Henrik
The workaround I was thinking of was to [for example, if the target is 30% as you say] set it to 32%, accept that, quit, quit, quit etc., so the FO2 is actually set at 32, ready to dive.
Then immediately repeat, setting it back to 30. If that doesn't reset the timer, I'd be more surprised than the behavior you previously described where going through the set screen but not storing a change doesn't reset it.