My Test Setup – SharePoint 2007 installed on box1, SQL 2005 installed on box2 Everything (services) runs on box1. SSP is http://box1:8888/ MySite is http://box1:8889/ Central Admin is http://box1:8080/ and the portal is http://box1/
Basically you have installed all web apps on the same host without DNS aliasing (for mysite, e.g http://mysite/).
With this setup SharePoint was crawling only the main Portal. Content in MySite was NOT being indexed. I did a full crawl, incremental crawl but no results were being returned from MySite.
I went into Shared Services Administration: SharedServices2 > Search Settings > Content Sources for “Local Office SharePoint Server sites” and guess What? Only “http://box1” was present in the “Start Addresses” section.