After upgrading, some Lion users reported a really disturbing problem with the built-in search system Spotlight: Only some of the files are being indexed.
Because my Mac also had this problem, I tried to resolve it and after a few hours googling about a solution I finally found a way to fix Spotlight.
About updating netatalk and adapting the configs
When you built your own NAS with support for the Apple Filling Protocol[^1] so you can access it the nice way via the OS X Finder and so Time Machine Backups on it, you are likely to use the netatalk package with its afpd and cnid_metad. With Lion, Apple updated the required AFP Version to AFP 3.3, which is not yet supported by most of the NAS out there[^2].
However, you’re fine when your using your own machine where you can compile your software by your own because you can simply use Version 2.2b4, which should be perfectly fine for your home setup.
Update 1: Version 2.2.0p6 (which is stable and should support Time Machine on Lion) is out, so I updated the guide. Thanks, Martin!
For the tips I’ll give you, I assume that you are already running a older version of netatalk, in my case it was 2.0.x.