Using the default template, I am getting this:
_MA_NAV_ACTIONS
and expands to:
_MA_NAV_VIEWACCOUNT
_MA_NAV_EDITACCOUNT
_MA_NAV_NOTIFICATIONS
_MA_NAV_LOGOUT
_MA_NAV_ADMINISTRATION

Where I should be seeing just the links.

XOOPS Version - XOOPS 2.3.1
PHP Version - 4.4.4
MySQL Version - 4.1.22-standard
Server API Version - cgi
OS Version - Linux

safe_mode - Off
register_globals - On
magic_quotes_gpc - On
allow_url_fopen - On
fsockopen - On
allow_call_time_pass_reference - On
post_max_size - 64M
max_input_time - 100
output_buffering -
max_execution_time - 100
memory_limit -
file_uploads - On
upload_max_filesize - 64M

This is on a duplicate site that I created to practice upgrading to 2.3.1. I created the site update.mysite.com, copied all of the files over and created a new database to which I imported all of the old data.

It is on this duplicate that I am finding the issue. Once I have it figured out, I'll take on the production one.

Old system was 2.2.4.

If I have bad files uploaded, is there a way of identifying them without uploading everything again?

I am seeing these errors on the page:

Notice: Only variables should be assigned by reference in file /modules/newbb/include/functions.ini.php line 70
Notice: Deprecated function 'mod_getunamefromids', use XoopsUserUtility directly. in file /Frameworks/art/functions.user.php line 26
Notice: Deprecated function 'mod_getunamefromids', use XoopsUserUtility directly. in file /Frameworks/art/functions.user.php line 26
Notice: Deprecated function 'mod_getunamefromids', use XoopsUserUtility directly. in file /Frameworks/art/functions.user.php line 26

In case another newbie encounters this, just overwrite the old default with the new one and the issue disappears with the old default theme.

Of course the upgrading instructions indicate to remove the /themes folder for I suppose obvious reasons but this leaves the old default theme which from my experience does not function properly with 2.3.1.