Someday, maybe. I really appreciate your comments and suggestions, but right now I will not spend hours if not days of my time trying to fix something which is already fixed. It works, all it needed was the second arduino and the probe loop fits neatly within one minute with plenty of room to grow and it will never interfere with the outputs, and if I ever need more room it's easier still to replace 750ms probes with 10ms probes and the problem is non existent again. I think it is better to spend your precious resources where they are really needed - and in my case this is development of new functionality. Right now I'm spending my time on integrating PIR sensors around the house, which will give my heating system more information, makes a good start for the security alarm, and makes possible funky ideas such as music following you around the house, ...
But I'm really grateful for the ideas - I'll put it on my TODO list and maybe one day I will rewrite the architecture to be event based with some sort of messaging system which is not serial like at the moment, please keep them coming.