I find Partition Magic to be excellent - except for merging partitions. It is best not even to attempt that. It is quite normal to get that warning, but there is nothing sinister about it. They're just covering themselves.
Did you make the new partition that you hoped to boot from "Active" when you created it? This option is found at the bottom of the "Operations" Menu under "Advanced" and is a bit obscure.
If you don't, you will get an error message such as "no operating system found".