I tried logging "$r->user()" to see if that was more reliable, but no
luck there either.
Apache 2.0.46 mod_perl 1.99_09 Perl 5.8.0
I haven't had any problems with $r->user() lately. And AFAIR Apache::AuthDBI worked for me with various 1.99 RCs before RC5, without Apache::compat.
But there's little point in reporting problems with an ancient development release like mod_perl 1.99_09. You might want to try to update to RC4 (which also requires an Apache update), or RC5, although the latter breaks compatibility with pretty much everything due to the namespace change.