all products from cart are removed when checking out as anonymous user

I'm having the same problem on my test enviroment.
The order is created and the email will send too but just the redirect for the anonymous user doesnt seem to work.
Instate of redirecting to the Checkout messages page the anonymous user gets the empty cart page.

Have you tried running update.php since your upgrade? Also make sure you check your Watchdog log to see if there are any obvious php errors.

I cannot reproduce the problem described in the original post on a clean install.

#2 is an entirely different problem, and a new issue should be opened for that if you can provide detailed steps to reproduce.

I can't reproduce this on the site linked in the original post either. If I add a product to the cart and then go to the checkout (either directly or via the cart page) I am redirected to the login page with "עליך להתחבר לפני שתוכל להמשיך לקופה." ("You must Sign in before you can proceed to Checkout.") at the top.

The problem is that I want the checkout process to display alll pages using SSL and not http, so when the anonymous user clicks the checkout button the page shifts from http to https and then the cart empties instead of displaying a message to the user to login.

I've only see this happening when going from http://www.site.com to https://site.com usually never had issues with going from http://www.site.com to https://www.site.com or http://site.com to https://site.com

Maybe something changed in Secure Pages. I remember when I was having the same issue a few years back I set up my SSL cert to be for https://www.site.com and in my htaccess I set up this to redirect all requests to include www.site.com

  # To redirect all users to access the site WITH the 'www.' prefix,
  # (http://example.com/... will be redirected to http://www.example.com/...)
  # uncomment the following:
  # RewriteCond %{HTTP_HOST} !^www\. [NC]
  # RewriteRule ^ http://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]

This is for D7/UC3 but should work for D6/UC2?

Well I added a SSL cert to the UC demo site at http://www.ubercartdemo.com and was having SSL issue. I'm using the Secure Pages module and what was happening (this didn't happen in D6/UC2) was that the cart was cleared for anonymous users when the url changed to https://domain.com/cart also clicking checkout would just bring me back to the cart page.

After some reading this is what worked on my server
Apache 2.2.21
DirectAdmin 1.40.3

I set up my cert for www.ubercartdemo.com so SSL works on https://www.ubercartdemo.com
I set up htaccess like this. I uncommented these lines

RewriteCond %{HTTP_HOST} !^www\. [NC]
RewriteRule ^ http://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]

In settings.php I added the following. When editing the settings.php file you might have to change the permission of the file to overwrite it and then change them back to what they were. Mine are set to 444 by default so had to change them to say 755 for editing and revert back to 444 after editing.

I edited
$cookie_domain = '.example.com';
to
$cookie_domain = 'www.ubercartdemo.com';

At the end of the file I also added

$conf['https'] = TRUE;.

From http://drupal.org/https-information

Drupal configuration

If you want to support mixed-mode HTTPS and HTTP sessions open up sites/default/settings.php and add $conf['https'] = TRUE;. This enables you use the same session over HTTP and HTTPS both -- but with two cookies where the HTTPS cookie is sent over HTTPS only. You will need to use contributed modules like securepages to do anything useful with this mode, like submitting forms over HTTPS and so on. While your HTTP cookie is still vulnerable to all usual attacks, a hijacked insecure session cookie can only be used to gain authenticated access to the HTTP site. It will not be valid on the HTTPS site. Whether this is a problem or not depends on the needs of your site and the various module configurations. For example, if all forms are set to go through HTTPS and your visitors can see the same information as logged in users then this is not a problem.

I installed and enabled Secure Pages module and set up the following settings

Non-secure Base URL
http://www.ubercartdemo.com

Secure Base URL
https://www.ubercartdemo.com

Pages which will be be secure
user
user/*
user/*/edit
admin
admin/*
cart*
cart
cart/checkout
cart/checkout/review
cart/checkout/payment_details/*
cart/checkout/complete

That should be it.

At this point, it seems the problem is with site configuration for the Secure Pages module. There doesn't seem to be an Ubercart issue here.

@end user: Perhaps you could look at the documentation page about Secure Pages setup for Ubercart, found at http://drupal.org/node/1445436, and see if you can improve it.

Actually just noticed the cart is still being cleared once in a while, looked at the server and drupal logs and nothing is showing up. Clearing out my browsers cache seems to fix the problem but it only happens once in a while and too tired atm to test it out some more.