How to configure boost for multisite configuration
Boost works out of the box with multi-site. If your cache files are being generated (they appear in /cache/normal/site1.example.org/), but not served (boost comment in the footer of the page, or X-Cached-By in the HTTP headers), then there is an issue with your .htaccess configuration.

You can debug your htaccess rules by enabling the rewrite log:

RewriteLog "/tmp/rewrite.log"
RewriteLogLevel 2


This can generate a lot of logs, use with great care in production.

Also check this post on how to debug htaccess rules:
https://stackoverflow.com/questions/9153262/tips-for-debugging-htaccess-rewrite-rules