I forgot to mention that I am also running Joomfish.
jfweblinks    ordered as 0
fsections     ordered as 0
jfrouter      ordered as -101
jfnewsfeeds   ordered as 0
jfdatabase    ordered as -100
jfcontent     ordered as 0
jfcontacts    ordered as 0
jfcategories  ordered as 0
jfalternative ordered as 0

Thank you for that information as it lead me in the right direction to fix my problem.

My main problem was that I not installed "Advanced Joomfish Language Aware Router (2.1)".
The plugin name seems to have changed from:
"system - JFsef" to "Joomfish - Pro Router".
It must be enabled and the "System - JFRouter" must be disabled.

I matched your order numbers as follows:
system - JFsef: -103
Joomfish - Pro Router: -103
System - MetaMod Pro: -102
System - JFRouter: -101
System - JFdatabase: -100
System - MetaTemplate: -99
[various others]
System - SEF: 15

and that cured all but 1 problem.

That problem was:
Only my frontpage menu items lost their itemIds.
My front page lets you choose the language in a menu and displays a different front page once you have chosen but the itemId from those choices were always null when SEF was turned on. They had valid itemIds when I turned off SEF in Joomla.

The code in the links is:
index.php?lang=en&option=com_content&view=frontpage
and
index.php?lang=fr&option=com_content&view=frontpage

Using the language code in the link automatically switches the language to either english or french.

To be able to add the language code in the link I had to establish the link using the "External Link" item type. If I used the more appropriate "Front Page Blog Layout" item type then I cannot change the link values because it becomes read-only.
Without SEF this works but with SEF it doesn't.

So to solve it, for SEF, I used "Front Page Blog Layout" item type and then went into the database menu record and modified the link to have the language code.

They produce different results basically because in the menu table:
"External Link" is type "url" and componentid = 0
"Front Page Blog Layout" is type "component" and componentid = 20

Thank you for your help.
Robert