User Role Editor multisite issue fixed with version 3.12.1 published at May 14th, 2013. While I continue work on version 3.14 and the good news that it is near to release, I had to release update for the current, 3.12, version. According to user obfuscated report at WordPress.org support forum (read this thread) that the feature “Apply to All Sites” stopped working after update to version 3.12. After quick check I confirmed the problem and published bug fix release 3.12.1 the same morning.
If you use User Role Editor under WordPress multisite environment and still sit on the version 3.12 or earlier, I have a strong recommendation for you – update to the latest version 3.12.1
Download link is here.
Additional change – starting from version 3.12.1 “Apply to All Sites” checkbox is available from the main site of the network only.