I just upgraded and ran into similar problems myself.
Alot of the problems can occur with cookie overlap issues.
Overlaps can occur in two scenarios:
1) old cookies stored from pre-upgrade with new cookie
2) from running multiple geeklogs on the same domain
To test if this is the case delete your cache and cookies and see if you still have the problem. (if not, I'll talk about another issue next)
In my case, I installed the new geeklog in different directory first so that I could test it out on a duplicate copy(renamed) of the database.
When swithching back and forth between the two I occasionall got SQL errors similar to yours. Clearing my cookies would temporarily fix this.
If your running 2 or more instances of geeklog you can make sure that all of your cookie names are different between the config.php files
PHP Formatted Code
$_CONF['cookie_session'] = 'gl_session'; // make unique like 'gl_session_site1'
$_CONF['cookie_name'] = 'geeklog'; // make unique 'geeklog_site1'
$_CONF['cookie_password'] = 'password'; // same as above, do the same for the rest
$_CONF['cookie_theme'] = 'theme';
$_CONF['cookie_language'] = 'language';
$_CONF['cookie_lastvisit'] = 'LastVisit';
$_CONF['cookie_lastvisittemp'] = 'LastVisitTemp';
In particular, both of your errors mention errors with "WHERE uid"
uid is retrieved from the cookie_name which tells me both of your config.php files have the same setting for this cookie. for years I had set this value to my site name. Now, after actually looking into this problem I discovered that it was actually referring to the username ie uid)clearing cache and cookies didn't fix it
Other errors still related to cookies is themes. Upgrading to the more current releases doesn't work with many of the old themes. You should set your default to professional in the beginning. But setting it in config.php will only help new and anonymous users. Even if you clear the cookie that pointed to the old theme, your personal default theme will still be stored in the database and will reset when you try to login.
Try these to things to fix this
1)in config.php turn off 'allow_user_themes' by setting it to zero
$_CONF['allow_user_themes'] = 0;
2)Backup your old themes (you should have already done this anyway)
make directories named after your old themes and copy the contents of the professional theme into them
Oh, yeah. There's also an FAQ.Geeklog FAQ - I can't login
Good luck! -Matthew Cox