ClickThrough on Google Webmaster Tool and also Traffic Source in Google Analytics

Here is one feasible circumstance.

• Google Webmaster Tools tracks searches and also clicks TO your domain name
• Google Analytics documents web page sights and also search phrases ON your domain name
• So in between leaving Google and also reaching your web pages with the GA tag, the search phrases are obtaining removed

Things to examine :

• Analytics is appropriately set up on every web page - see to it the monitoring tag in operation on the homepage is that like the inner web pages
• You could have JavaScript reroutes that are removing out the referrer and also search phrase details - surf your website with JS impaired and also see if every little thing acts effectively
• You could have meta - rejuvenates that are rerouting site visitors and also shedding the referrer details. Disable meta-refreshes and also attempt surfing the website.
• You could have some server - side reroutes that strip the referrer details - usage a device like redbot.org to see what headers are being returned when you request your website

Update : below is my common simple.htaccess. I've changed it for your instance to reroute to Home.html. Allow me recognize if it functions.

Update 2 : I've included the redirect to www. based upon Paul Irish is HTML5 Boilerplate, which has one of the most comprehensive.htaccess I recognize :

# ----------------------------------------------------------------------
# Start rewrite engine
# ----------------------------------------------------------------------

# Turning on the rewrite engine is necessary for the following rules and features.

<IfModule mod_rewrite.c>
  RewriteEngine On
</IfModule>


# ----------------------------------------------------------------------
# Suppress or force the "www." at the beginning of URLs
# ----------------------------------------------------------------------

# The same content should never be available under two different URLs - especially not with and
# without "www." at the beginning, since this can cause SEO problems (duplicate content).
# That's why you should choose one of the alternatives and redirect the other one.

# By default option 1 (no "www.") is activated. Remember: Shorter URLs are sexier.
# no-www.org/faq.php?q=class_b

# If you rather want to use option 2, just comment out all option 1 lines
# and uncomment option 2.
# IMPORTANT: NEVER USE BOTH RULES AT THE SAME TIME!

# ----------------------------------------------------------------------

# Option 1:
# Rewrite "www.domain.com -> domain.com" 

<IfModule mod_rewrite.c>
  RewriteCond %{HTTPS} !=on
  RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
  RewriteRule ^(.*)$ http://%1/$1 [R=301,L]
</IfModule>

# ----------------------------------------------------------------------

# Option 2:
# To rewrite "domain.com -> www.domain.com" uncomment the following lines.
# Be aware that the following rule might not be a good idea if you
# use "real" subdomains for certain parts of your website.

# <IfModule mod_rewrite.c>
#   RewriteCond %{HTTPS} !=on
#   RewriteCond %{HTTP_HOST} !^www\..+$ [NC]
#   RewriteCond %{HTTP_HOST} (.+)$ [NC]
#   RewriteRule ^(.*)$ http://www.%1/$1 [R=301,L]
# </IfModule>

# Installation directory
RewriteBase /

# Protect hidden files from being viewed
<Files .*>
    Order Deny,Allow
    Deny From All
</Files>

# Allow any files or directories that exist to be displayed directly
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

# Rewrite all other URLs to Home.html
RewriteRule .* Home.html [PT]

Note : you'll need to relabel or delete the existing index.html for this to function.