First, to be clear, I know El Capitan is in beta and I do not expect you to support prerelease software. I'm sure that it's crazy annoying to get flooded with support requests for something that isn't stable and hasn't even been released yet.
With that said, I am experiencing a problem with Alfred on El Capitan and wanted to offer any assistance in troubleshooting if it can be of any assistance to you.
The issue I'm having is that any time I exit Alfred and restart it Alfred seems to lose most of it's settings.
Every time I restart it looses settings like custom hotkeys, search scopes, custom searches, themes and advanced appearance settings all seem to be reset to the defaults. However, workflows, sync folder, Powerpack license and usage are all carried over just fine.
It doesn't look like /Users/cwhite/Library/Application Support/Alfred 2/Alfred.alfredpreferences is getting updated while exiting or relaunching, the last change time was from this afternoon before I updated to El Capitan.
Setup notes: I did an update install from Yosemite. I am on Alfred 2.7.1 (387). With the exception of iStat Menus everything I've tried this evening since updating has worked as expected though I did have to re-enable some apps to launch at startup.
If I can do anything to help please let me know how, otherwise keep up the incredible work you do on Alfred!