My Alfred preferences are not stored on my boot volume. They are stored on a a direct-attached SAS volume that is mounted on login (it is APFS encrypted - but previously HFS journaled, encrypted with the same behaviour).
Despite this, Alfred will not load my preferences if it is setup to start on login.
I must quit Alfred and re-open it for the preferences to be read/respected. The easiest telltale is that when my system starts/reboots Alfred shows the default grey, rounded, fat-border theme, and my preferences indicate the Frosty Teal theme; also my workflows don't work until Alfred is restarted because they're all loaded with my preferences.
I'm on 10.13.6 and alfred 3.6.2 (922), the volumes are on a DAS SAS disk set. This has never worked - IE it's been at least a year or two, but I decided it's time to report it.
I believe Alfred should wait for drives/volumes to finish mounting on login before attempting to load preferences, or at least check to see if the preferences are available or maybe even keep some kind of shadow/cached copy in the user's library folder?