Maybe you could group the lines and then have better luck with arranging them. Personally I would go with different layers - much easier to control and no guessing where they lie in the hierarchy.
Beyond that - you've done some really nice animation work Liron
I'm creating illustrations for stock websites (such as shutterstock) which means there are certain rules I have to follow, such as converting those lines to fills eventually, and groups cause issues sometimes when creating old EPS, but I will try this option.
still, it's kinda stupid that if I color them is the order from most behind to most above, it works out. If I change color it's fixed, but then changing back to previous color brings the problem back - looks to me more like a wrong behavior of the software.
If there's no solution, I will try to report this as bug or something.
Ok, so grouping doesn't help cause when I eventually need to convert lines to fills (it's a must for stock websites) I need to un-group my lines and then I go back to square 1, I just tested it.
So separating to layers is the only option for now.
Unless I'm missing another option (if anyone knows please reply) I will just send a feature suggestion to adobe and hopefully they will fix it.