Ok I've narrowed it down to one file - this is what I did:
1. I created a fresh java project on Helios
Then I created a test xhtml file
Result: Content Assist Does not work
2. I restarted Helios and opened it again
Result: Content Assist Does not work
3. I opened Galileo and open that same workspace and file
Result: Content Assit Works!
4. So I then proceeded to open this same file and workspace back in Helios
Result: Content Assit Works also!
I took snapshots of the files in step 2 and 3 and did a diff.There was a difference between .\.metadata\.plugins\org.eclipse.core.resources\.projects\***\.indexes\properties.index
So what I did was repeated step 1 and 2 with a different project name - and then i proceeded to copy the properties.index file over to this new project location and guess what?
Result: Content Assist Works!
So the workaround at the moment seems to be opening up the project in galileo and then reopening it up in helios.