As I have not written or tested multiple spider code, I'm not sure of the changes needed or whether things would work from shell. The only things I can suggest are the ideas already mentioned. One thing you could try is running the following from shell and see what happens. Make a database backup beforehand just in case.
Code:
nohup php -f spider.php htp://www.domain1.com > log1.txt &
nohup php -f spider.php htp://www.domain2.com > log2.txt &
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