Light Flow Issues:
Per our earlier discussion on this, I emailed the dev, and after a few emails back and forth, got this helpful one from him, so thought I'd pass it along:
Well I've been using ICS with the app myself since October (Uk release date of gsm galaxy nexus) and apart from not been able to hook into clearing single notifications by swiping it seems to work well.
For the "alway on" issue. That came from a bug in the previous version of the app when upgrading some settings when it moved from having 1 flash speed for the whole app to 1 flash speed per notification.
If you go into one of the notifications, switch it to another value and back again this should reset the issue and clear it.
My be try disable "pulse notification light" in the phone settings --> display and check it on again.
Also make sure you've no outstanding notifications up when you start the app. If another app "gets in first" with a notification, then lightflow can't control it. Because lightflow raises a notification on bootup for most people this should work fine, but maybe there's another app that's starting up quicker and stealing access to the led.