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If you don't show us the contents of file1 and file2, we can only guess at what might be going wrong. Are there any empty lines in file1 and file2?

I don't understand the problem. Don't:
program_to_produce_input | awk -F ': *' '
function p(){
if(host=="")return
printf("%s\t%s\t%s\n",node,host,agent)
host=agent=""
}...

Without knowing your input:
awk '/AP/{sub(/:80/, "", $4);printf $4"\t"} /User-Agent/{sub(/^[^:][^:]*:/,"");printf $0}/Host/{sub(/^[^:][^:]*:/,"");print}'