Oh, so you're just asking if HP might suck somehow? The answer there is yes...
Dell does this kind of crap much less often than HP in my experience, but both are known to make highly customized cable assemblies for their servers, and these can go wrong if they are not used as intended. It also makes for wicked hard debugging over the Internet. To give you an idea what I mean, take a look at
this eBay listing for your controller that includes a cable harness.
Now if you look at the two cables plugged into the controller, you see that there is one that fills out the full width of the connector ("Port 2") and another that is only half-width ("Port 1"). If you follow these out to the connectors, you see the wider one services two connectors.
Because some of the SAS lanes on Port 1 have been abandoned, it might not be odd that they could have been abandoned in firmware or disabled by configuration in order to prevent the RAID card from complaining about or wasting time probing them. So the very first thing I would do if I were you would be to make certain that your cabling is correct. I can't say for certain that Port 2 is supposed to have the dual cable on it (I'm basing all this on an eBay photo after all), but if Ports 1 and 2 got inadvertently switched around, I can see lots of room for trouble here.
You may also want to completely reset your controller to see if it suddenly picks up the "missing" drives.