JS and CSS paths are incorrect (Page not Found)

Very similar issue to #574952: Styles not working except installation is on a Linux (CloudLinux) server instead of WAMP and I am using Pressflow instead of Drupal Core.

I have noticed the following Page Not Found errors in dlog:

1.  Location: http://site1.domain.com/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/medium.css
Referrer: http://site1.domain.com/forum
Message: home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/medium.css

2.  Location: http://site1.domain.com/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/large.css
Referrer: http://site1.domain.com/forum
Message: home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/large.css

3.  Location: http://site1.domain.com/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/normal.css
Referrer: http://site1.domain.com/forum
Message: home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/normal.css

4.  Location: http://site1.domain.com/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/template/forum_fn.js
Referrer: http://site1.domain.com/forum
Message: home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/template/forum_fn.js

5.  Location: http://site1.domain.com/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/template/styleswitcher.js
Referrer: http://site1.domain.com/forum
Message: home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/template/styleswitcher.js

Checking the Page Source from http://site1.domain.com/forum, I can see there incorrect paths:

<script type="text/javascript" src="/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/template/styleswitcher.js"></script>
<script type="text/javascript" src="/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/template/forum_fn.js"></script>

<link href="/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/normal.css" rel="stylesheet" type="text/css" title="A" />
<link href="/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/medium.css" rel="alternate stylesheet" type="text/css" title="A+" />
<link href="/home/domain/public_html/pressflow/phpBB3/styles/prosilver-embed/theme/large.css" rel="alternate stylesheet" type="text/css" title="A++" />

In Server URL Settings:

Force: yes
Server protocol: http://
Domain name: site1.domain.com
Server port: 80
Script path: /phpBB3

In settings.php:

$base_url = 'http://site1.domain.com';

In phpBBforum settings:

phpBB forum root path: /home/domain/public_html/pressflow/phpBB3/
Path to phpBB api file: sites/all/modules/phpbbforum/includes/
phpBB api file name: phpbb_api.php

I also have URL aliases like INSTALL.txt:

forum/files.php -> phpbbforum/files.php

In phpBBforum settings, I tried using phpBB3/ for the root path. That fixes the above errors but creates another list of problems with the URL to the small images like:

http://site1.domain.com/http://site1.domain.com/phpBB3/styles/prosilver-...

Any idea where I should look?