I think this is a bigger issue.
A manual (re)install does solve this error message, but NOT if running multiple wordpress installs as individual domains, but as a sub-domain of a primary web hosting account.
I run wordpress on my blog, which is its own domain (www.blognamehere.com)
My web host allows me to run other domains (www.websitenamehere.com) under the same hosting accounting account, although officially they are subdomains of my primary account (www.blognamehere.com).
Orginally I used simplescript to upgrade all of my wordpress installs; the primary account domain (www.blognamehere.com) upgraded fine, no breaks; but auto-upgrading http://www.websitenamehere.com fronm 2.9.b to 2.9 repeatedly resulted in the error "Call to undefined function is_admin() in /home/blognamehere/public_html/wp-includes/vars.php on line 16."
not that excited about doing a manual install, i instead decided to do a totally new, clean install of 2.9 in websitenamehere.com's directory; clean install was fine until i imported orginal mysql db into new install/db - once again could not shake the error message "Call to undefined function is_admin() in /home/blognamehere/public_html/wp-includes/vars.php on line 16."
i then followed in painstaking detail the instructions on this thread to manually upgrade websitenamehere.com; including as usual changing in that directory the memory limit in wp-settings.php (from 32 mb to 128 mb).
result: websitenamehere.com is now running 2.9 and seems to run fine.
HOWEVER - that then broke the already upgraded (and working fine) 2.9 wordpress install in my primary domain (blognamehere.com), with the same error message: "Call to undefined function is_admin() in /home/blognamehere/public_html/wp-includes/vars.php on line 16."
i then manually upgraded blognamehere.com; which now works ONLY if the wp-settings.php memmory limit in that (primary) directory remains at 32 mb; and breaks again if that wp-settings memory limit is increased beyond 32 mb.
Prior to the upgrade from 2.9b to 2.9, the wp-settings.php file in all my domain directories (primary, and add on domains running as subs of the primary) were set to a memory limit of 128 mb memory - and all ran fine.
Unfortunately I need to be able to set all wp-settings.php memory limits to 128 mb in order to maintain functionality of each wordpress installs' individual plugins.
Any suggestions/thoughts, and/or is there a workaround for the apparent restrictions on increasing the memory limit above 32mb in the primary wp-settings.php directory?