Godaddy internal server errors

.htaccess - no changes and the files on both servers are same.

Both the sites are on different servers (different IPs).
Production one is http://www.mydomain.com and
copied one is http://dev.mydomain.com

I have the drupal install in a subdirectory in the html directory. I didn't have to uncomment the RewriteBase line in .htaccess.
Interesting thing is both the sites were working for many months now and only giving these error for the past 3 weeks.

This is the .htaccess in the html directory
-------------------------------------------

addhandler x-httpd-php-cgi .php4
addhandler x-httpd-php5-cgi .php
addhandler x-httpd-php5-cgi .php5

RewriteEngine on
RewriteRule (.*) med/$1 [L]

First 3 lines added by godaddy tech support while disabling fast cgi.

.htaccess in my drupal directory (med)
------------------------------------------------
#
# Apache/PHP/Drupal settings:
#
# Protect files and directories from prying eyes.

Order allow,deny

# Don't show directory listings for URLs which map to a directory.
#Options -Indexes

# Follow symbolic links in this directory.
#Options +FollowSymLinks

# Make Drupal handle any 404 errors.
ErrorDocument 404 /index.php

# Force simple error message for requests for non-existent favicon.ico.

# There is no end quote below, for compatibility with Apache 1.3.
ErrorDocument 404 "The requested file favicon.ico was not found.

# Set the default handler.
DirectoryIndex index.php

# Override PHP settings. More in sites/default/settings.php
# but the following cannot be changed at runtime.

# PHP 4, Apache 1.

php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_value mbstring.encoding_translation 0

# PHP 4, Apache 2.

php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_value mbstring.encoding_translation 0

# PHP 5, Apache 1 and 2.

php_value magic_quotes_gpc 0
php_value register_globals 0
php_value session.auto_start 0
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_value mbstring.encoding_translation 0

# Requires mod_expires to be enabled.

# Enable expirations.
ExpiresActive On

# Cache all files for 2 weeks after access (A).
ExpiresDefault A1209600

# Do not allow PHP scripts to be cached unless they explicitly send cache
# headers themselves. Otherwise all scripts would have to overwrite the
# headers set by mod_expires if they want another caching behavior. This may
# fail if an error occurs early in the bootstrap process, and it may cause
# problems if a non-Drupal PHP file is installed in a subdirectory.
ExpiresActive Off

# Various rewrite rules.

RewriteEngine on

# If your site can be accessed both with and without the 'www.' prefix, you
# can use one of the following settings to redirect users to your preferred
# URL, either WITH or WITHOUT the 'www.' prefix. Choose ONLY one option:
#
# To redirect all users to access the site WITH the 'www.' prefix,
# (http://example.com/... will be redirected to http://www.example.com/...)
# adapt and uncomment the following:
# RewriteCond %{HTTP_HOST} ^example\.com$ [NC]
# RewriteRule ^(.*)$ http://www.example.com/$1 [L,R=301]
#
# To redirect all users to access the site WITHOUT the 'www.' prefix,
# (http://www.example.com/... will be redirected to http://example.com/...)
# uncomment and adapt the following:
# RewriteCond %{HTTP_HOST} ^www\.example\.com$ [NC]
# RewriteRule ^(.*)$ http://example.com/$1 [L,R=301]

# Modify the RewriteBase if you are using Drupal in a subdirectory or in a
# VirtualDocumentRoot and the rewrite rules are not working properly.
# For example if your site is at http://example.com/drupal uncomment and
# modify the following line:
# RewriteBase /med
#
# If your site is running in a VirtualDocumentRoot at http://example.com/,
# uncomment the following line:
# RewriteBase /

# Rewrite URLs of the form 'x' to the form 'index.php?q=x'.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]

# compress text, html, javascript, css, xml:
AddOutputFilterByType DEFLATE text/plain
AddOutputFilterByType DEFLATE text/html
AddOutputFilterByType DEFLATE text/xml
AddOutputFilterByType DEFLATE text/css
AddOutputFilterByType DEFLATE application/xml
AddOutputFilterByType DEFLATE application/xhtml+xml
AddOutputFilterByType DEFLATE application/rss+xml
AddOutputFilterByType DEFLATE application/javascript
AddOutputFilterByType DEFLATE application/x-javascript

# $Id: .htaccess,v 1.90.2.5 2010/02/02 07:25:22 dries Exp $