Hey Epad,
It could be that I've just woken up, but I'm a tad confused as I read this. It seems like your messages should be doing the job you would intend them to do (making the player finish them before the timed warps can occur). I have Messages Disappear checked in Eiyuu and such, and have never had an issue with this. You let the player read the message, the string ends, the message disappears, and then the timed warp can kick in.
If you want that process to happen, you should add the Messages Freeze All Action rule. This forces the message string to have to end before the timed warps can come into play. (In other words, it prevents the timer from starting too early.)
It's also a minor thing, but you could also allow enough ticks before the timed warp occurs. (I'm not sure if there's "too few" you can have to where the warp activates before the string or something else but this was something Moosh taught me.) I always put in around 8 ticks for an "instant" warp once the cutscene is done.
Edited by Teamudf, 13 August 2014 - 11:00 AM.