Thanks for the info Paul.

I guess you have Ha configured for Autofocus on filter change but L not set to Autofocus on Filter Change.

I think you're options are:
1. Fix not being able to align on Ha. My guess it that you have exposure set too short (probably set appropriately for L) so the stars are too faint on Ha. So you can increase the exposure and / or gain. I use roughly a x5 exposure factor for narrowband so if you use 2s for L to align you may need 10s on Ha (depends on filters of course so may be different on your setup).
2. Turn off Ha focus on filter change. The scheduler will still Focus on startup. You may need to think about your 120min refocus setting depending on what you're doing.

Read More...