So I picked up an H240 on eBay for a good deal and I was hoping to use it with FreeNAS, and I've noted the same issue. My original intent was to boot up in CentOS 8 and virtualize FreeNAS and passthrough this HBA to FreeNAS along with a one of the ports on my 1/10GbE adapter. The first issue is that the card takes ages to initialize, 20 seconds or so during the boot of the host OS and then several minutes when passed through to the VM eventually failing but continuing to FreeNAS.
I discovered the same thing, too. Only the ports that are populated during boot appear to "work" as expected (hot pluggable) but it's as if the ports that are not occupied during boot are disabled, like some sort of power saving feature, not sure. This HBA also doesn't seem to be exactly transparent to FreeNAS when it's running in a VM, either. Nothing about the drive appeared (SMART status, type, statistics, serial, etc). Although the hot plug issue persists even with FreeNAS running bare metal with the card. It might be a driver issue in freeNAS because I seem to recall that it worked as expected in CentOS 8 with the proprietary drivers loaded.
I'm kind of skeched out about using this HBA for FreeNAS, what are some good cheap ones that aren't very old? (I picked this one up on eBay for $30 thinking it was a steal if I could get it to work as expected)