Finally got it working.

I am using mod_rewrite and an .htaccess file to enable SEO under Joomla. Since Joomla is rewriting all the links in real time I think it was confusing PAP4.

I had to change my tracking links under PAP4 configuration to:

SEO links (with mod_rewrite)

In case anyone else has this issue.

Detailed instructions:

1. Log in to PAP4 as admin

2. Click on the Configuration link on the left menu

3, Click on Tracking Settings

4. Scroll down to Affiliate linking method

5. Click the checkbox next to SEO links (with mod_rewrite)

6. Click the "Continue Setup" button on the right of the demo URL

7. Make sure the SEO Links settings are correct

8. Copy the customized .htaccess code in the text window and save it to your clipboard

9. Add it to your .htaccess file (I had to add it above my Joomla code)

Now the cookie should be set and recognized correctly if all the other configuration data is set correctly. My affiliates now have a custom URL that looks like this:

www.mysite.com/ref/testaff.html

which takes their referrals to the main page of the site. All sales and clicks are being recorded correctly to generate commissions.

Thanks for all the help...

Hi palikari, Just read this post and thanks in advance I am about to embark on a cbsubs + PAP4 implementation with SEF urls turned on so you just gave me a heads up.

Just a question for you if thats ok, with SEF urls turned on and using the PAP tracking module is can is it possible to track clicks from any page on your site, on a content article for eg? If so what sort of format would the affiliates url need to be?