Really happy. Indesign CS6 behaves normally on Sierra and Java6. El Capitan/Indesign is now a past nightmare for me.

Kate, did you restart your computer after installing Java SE 6 ?

@ P Jones : did you try to trash Indesign preferences ?

I must confess however that despite replacing Java and trashing prefs, the tool panel has now a rather evanescent behavior when I move it. That is much better than before, but still frustrating.

Expand the file “javaforox-2.dmg”. Java SE 6 is inside.

After re-installing Java SE 6, I had the classic problem of the blank character palette. Then I trashed Indesign prefs and now all seems as normal as it can be.

No problem with Illustrator. No crashing (till now) with Indesign, but openning and switching between palettes VERY slow.