Does your ROM includes a theme system? If so, that's the cause...
I've been looking for an answer too and I found this thred at GitHub. I haven't post much so I have no rights to post URLs as links for now... Please copy paste the following link:
There we can read the following:
Originally Posted by rovo89 commented on 19 may 2014
ok, that's it then. Some roms have theming engines that conflict with xposed. I'm looking for solutions, but meanwhile, please use the "disable resources api" setting in the installer. You might not be able to use some modules, but most should still work.
Doing so enables Xposed and that rebooting red message dissapears. However many modules are not functional if this adjustment is set in the configuration, so it's useless...
As far as I understand, there is no fix forthat issue then. So you can try another ROM with no themes system.
I hope this has been helpful for you =)