LP Version: 4.4.31
Platform: Paper
Version: 1.14.4

I have recently disabled vanilla OP and have started using the auto-op feature from luckperms. It seems to work fine for the permissions of most plugins, however, it does not work for luckperms permissions. I don't think it's just luckperms.autoop either; I have given myself specific luckperms perms and those don't seem to work either. I have tried relogging and doing /lp sync but to no avail.

There’s a config option that determines whether LP respects OP or not. Pretty sure that’s off by default.

The option is true (on) by default.
Give yourself luckperms.* and try again.

It is already enabled and I have tried giving myself luckperms.*. It still does not work.

You can check what's going on with the verbose command.

https://github.com/lucko/LuckPerms/wiki/Verbose