Turns out my recent post was kind of correct, but not fully. It seems that now you need both of the flags to make everything work. So start chrome with both
--allow-file-access-from-files and it should work.
On Ubunut just fire up the Main Menu editor under System->Preferences to make that easy.
Sadly the upgrade and import for tiddlywiki over the web are still not working and so I switch to firefox for that.