[TYPO3] Big upgrade to rc2 problem - update error, and no page tree

[Jody Cleveland]

Hello,

I just upgraded one of my sites to ver. 4 rc2 from 3.8.0. I'm running
this site on a redhat 4.0 AS server.

My process for upgrading was, I created a new directory for the source,
and a new one for the dummy content. I just took the two straight from
the download page off the typo site. Then, I did a dump of the database
from my existing site to a new database. In the install tool for the new
version, I picked that new database and performed the update wizard. All
went fine.

I then logged into the backend, and this notice was on the screen:
- The Reference Index table is empty which is likely to be the case
because you just upgraded your TYPO3 source. Please go to Tools>DB Check
and update the reference index.

So, I went to Tools - DB check, and clicked the button for Update now!
That seemed to go fine, and had this output:
Reference Index Updated
1508 records from 23 tables were checked/updated.
.....

So, I cleared the cache and logged out. On logging back in, I get that
same error message. And, I also noticed that my entire page tree is
missing. So, I went back to DB check, and looked at Record Statistics.
Which, gave me this:

Pages:
	Total number of pages:		116
	Hidden pages:		4
	Marked-deleted pages:		Array
Document types:
	Standard (1)		103
	Advanced (2)		1
	External URL (3)		7
	Shortcut (4)		3
	Not in menu (5)		0
	Backend User Section (6)		0
	Mount Point (7)		0
	Spacer (199)		0
	SysFolder (254)		2
	Recycler (255)		0

Also, I looked at Total Page Tree in there, and that does show the
entire tree.

So, I have two questions. One, why do I continue to get that message
each time I log in, even though I've all ready updated it? And, two, how
do I get my page tree to display again?

- jody