Can you check all of your rsl files to see if you have any CFL errors in them? You can issue the command:
grep cfl rsl*
If any show up, try decreasing your time step to something more like 4xDX.
There are a couple other things that could be causing issues.
1. Domains 3 and 4 are too small. No domain should ever be smaller than 100x100 grid points (e_we X e_sn).
2. Because your domains are small, you probably don't need to use 60 vertical levels. Try to decrease this back to the default value of 45 for each domain.
Take a look at this page that provides best practices for setting up your domain.