Ya I found it to be a good idea to do the major setup of jambadev from a clean install of the addon, and then doing a /reload to make sure everything still looks the same, prior to logging out and back in to save all the settings for sure.
It's still being tested in a beta type stage, so I'm willing to do a little extra work and I'm sure the settings update/saving hiccups will be ironed out before it's officially released.