I just installed Eclipse Neon on a Linux Mint 18 machine. And discovered that tooltip windows were using a weird color theme: dark blue foreground on black background. I tried several tricks I found on various websites, without success. In the end, I found this one, which seems to work (but I have not used Eclipse in this new configuration for long enough):
I added the following two lines in the eclipse.ini file:
--launcher.GTK_version
2