@art_director_simmons: same here. I have updated to 10.11.1 hoping it would fix it but same as before.
@larry g.schneider: after removing preferences, the right click returns (same as stated before) and on restart of illustrator right click disappears (as already mentioned before) - so same situation persists.
@james pageau: Brilliant! This has now fixed the issue.
For those interested:
1. open automator
2. create new workflow and choose "Folder Action" for type of document
3. where it says "Folder action receives files and folders added to" choose the folder WSMgrCfg (found in library/preferences/adobe...19/en_us/WSMgrCfg)
4. in the left side, choose "Files and Folders" to short list the actions
5. drag "get specified finder items" and click the "Add..." and choose the file called WSMgrCfg in the folder WSMgrCfg (it's the white file with no extension)
6. drag "move finder items to trash"
Save this workflow with any name you want such as "refresh illustrator" (anything)
And quit.
Now, it will delete the file anytime it finds it. You might want to delete the file (not folder) to get it started.