I've been working on my calling script while reading this post and watching the concerns and possible problems present themselves. I personally use post-it flags because I can designate a color for each group (Lights=chartreuse, Projections=Teal, Deck=Pink, Important Raft Moves=Green, Warnings=Primary Blue, Stand-by=Primary Yellow). However after reading about the concerns of cues running away I started to look for fixes. So far the best I've come up with is that I use the post-it labels , which are sticky all over and thus less likely to fall out, to list my warnings and stand-bys on. This way I'll be at least aware that something in a sequence is missing.
Something else I did this time was to use reposition-able glue dots on the post-its that were normal. They were a bit of a pain at the start but after a few dots I got used to the process and it became less time consuming. I'm still trying to figure out a way to be sure my flags are more stable, but so far this has been my solution.