This is quite normal in one's first try with dense filters. Now you'll need to edit your FilterInfo.txt file to get brighter stars when autofocusing H-alpha.

For a very clear example of how to do this, look for ACP's help page "Extended Filter Support". That page's section "Setting Up Focus Offsets the Easy Way" shows how you can customize your configuration file "FilterInfo.txt" so that H-alpha and other dense filters use a brighter star. That worked for me.