Changes in test version applied in live version as well On a D6 multisite setup, under the sites folder, there are a bunch of sites. Two of which are the sites testsite.domainname.com and domainname.com.
They have the folder structure I put at the bottom of this post.

So the problem is that changes made in the test version also seem applied to the live version, obviously with very 
undesired results for the end users. 
I checked the settings.php file to see if the same database would be connected to but the 
data in both files are for different databases. 

Changes applied to the test server that unintendedly have an effect on the live site 
are not only limited to changes in the domain_custom.module file. 
I noticed that changes made on the testsite in the page.tpl.php did the same thing; 

testsite.domain.com
-modules
--domainname_custom
--nice_menus
-themes
--custom_theme
-settings.php  

domain.com
-modules
--domainname_custom
--nice_menus
-themes
--custom_theme
-settings.php
Of course i have to ask the obvious here, did you check out multi-site install