I'm working on a site with a sub-theme based on Omega 4.x (it's used 4.0, 4.1, and 4.2) and uses the mailsystem module. I've been seeing problems much like those described in [#6790982], #2051135: Mail System breaks theme registry and #1613562: Mail System breaks Omega based theme. In particular, I get plenty of "array to string" warnings when template files print variables, missing classes on wrapper elements, and -- before I removed all use of layouts -- layouts not being used.

When the problem occurs, the cached theme_registry does not list all the omega preprocess functions, etc.

I can't tell whether mailsystem or omega is a fault but there seem to be enough patches to around so I'll just leave this issue here just in case it is Omega that needs to be fixed.