Q: Mail viewer window keeps disappearing.

Boot into the Recovery Drive by holding down Command R when restarting.

Run Repair Drive and Repair Permission in Disk Utility on the Repair Drive.

Restart

Download and run the combo updater to refresh your OS X files.

OS X Mavericks 10.9.3 (Update (Combo)

http://support.apple.com/kb/DL1746

Great! Glad I could help.

Kurt Lang's site is great resource for Fonts. See his info on Suitcase.

Font Management in OS X, by Kurt Lang

http://www.jklstudios.com/misc/osxfonts.html

Tried this but it still does not work.

apparently it had to do with trusting a certificate.  I do not but selected trust ,only because I wanted to read my mail.

I am having the same disappearing message window issue running Yosemite 10.10.1.  I have tried disk repair/permissions repair with no luck.  Mine will open when the "Use Classic View" is checked in preferences but disappears if you uncheck it.  Any other suggestions?

Having similar problems.  Some additional symptoms:

- There was a Mission Control desktop (Space) for which the menu bar was blank.  Being suspicious, I removed it.

- Even though applications are assigned to specific desktops/spaces, clicking on their Dock icon doesn't switch to that desktop/space. Instead, the app is activated and its menu bar appears in whatever desktop/space I'm currently in.

          Mission Control preferences are

                    (unchecked) Automatically rearrange Spaces ...

                    (checked) When switching to an application, switch to ...

                    (checked) Group windows by application

                    (unchecked) Displays have separate Spaces

I had this issue too. For me the fix was uninstalling the Mail Act-on add-on to the mail app.