with the past few EAP releases I noticed that changing font+color settings are not being written to disk. How to reproduce:
1) go to File->Settings->Editor->Colors and Fonts->Language Defaults.
2) Take the current scheme and "Save As" to another name.
3) Make a change to a setting in the new name scheme.
4) Notice that the change did have an impact in the current editor window.
5) Exit and restart Intellij. Notice the change made has been lost.
6) Diff the .icls file produced by Intellij. The file differ by just the scheme name:
nrinydev$ diff alan.icls alan2.icls
< <scheme name="alan" version="124" parent_scheme="Default">
> <scheme name="alan2" version="124" parent_scheme="Default">
PS I'm running on linux, JDK8_40, Build 141.177