Well here's what I noticed - If I set any $ENV{anything} on Apache startup in Perl code, it gets wiped out after the first use per PID just like the MOD_PERL environment variables, but if I use SetEnv it doesn't.

I don't know what/why they are being removed -- perhaps it's even in some .so. Regardless, my workaround is to add:

SetEnv MOD_PERL_API_VERSION 2
SetEnv MOD_PERL 'mod_perl/2.0.6-rc2'

to my httpd.conf.

Thanks.