I just now found out that when spam reaches my ispconfig 3 server, it is bounced, or deleted. I did the GTUBE test, and never received it with a header of ***SPAM***. How do I fix this? I know its an option in /etc/amavisd/amavisd.conf
No. You can set the level for marking spam in ispconfig. Take a look at the spamfilter policies and select e.g. the spamfilter rule "normal" for the mailbox.
Then you should enable debugging in amavisd.conf and restart amavisd. In the mail log you will find then detailed information about what amavisd is doing.