A few weeks ago I actually had someone come into my house while I was there and systematically check each group of containers. I booted the player because, while I think I set all my secures, who knows, right? And the player scampered away because she was being attacked by some sort of monster outside the house, hehe.
I didn't read the whole thread, and I doubt anyone will read this post, but quite simply, if you ever customize your house you need to check everything that has a security function to see if it reset. Doors and teleporters the like will reset I think every time, not sure about containers, but general rule of thumb is to check everything--dye tubs, coops, etc--after you custom. It's a pain, but it's the only safe thing to do. Unless there is bug beyond that, I don't know what else to offer. It's the kind of thing where not being able to discuss bugs here creates an information void...