path
I'm using 32 bit, but the result seem almost the same:
/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
I think sa-update only for updating spamassasin, so it should not affecting the installation.
Maybe it's a permission problem. What user do you use, root or something else?
Why don't you try to check install log? It should be in /var/log/ispconfig3_install.log
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