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So I created both pools for each domain with the following configs:

[domain.com]
listen = 127.0.0.1:9001
listen.allowed_clients = 127.0.0.1
user = user1
group = group1
pm = dynamic
pm.max_children = 50
pm.start_servers = 20
pm.min_spare_servers = 5
pm.max_spare_servers = 35
chdir = /

[domain2.com]
listen = 127.0.0.1:9002
listen.allowed_clients = 127.0.0.1
user = user2
group = group2
pm = dynamic
pm.max_children = 50
pm.start_servers = 20
pm.min_spare_servers = 5
pm.max_spare_servers = 35
chdir = /

And created the linux user with useradd and well placed their files and confingured nginx to work at /home/user rather than the regular /srv/www.

Why even with this do I get mkdir() permission denied on one site but not on the other? Am I missing some other config too?

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What OS are you using and is SELinux enabled? –  Wesley Mar 26 '13 at 23:03
    
@WesleyDavid SELinux fully disabled under CentOS 5 32bit –  Lucas Gomez Mar 26 '13 at 23:08
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