I´ve put the Intel NIC (X4) into the X16 slot (so no hardware mod needed).
I´m also using the the customized bios to get the 6 SATA ports. I got it from here: https://www.bios-mods.com/forum/Thread-HP-Proliant-Microserver-AMI-BIOS-MOD. I Think i use the 2011 version. To my knowledge there are only 2 Bios Versions: 29/07/2011 and 01/10/13 originaly released by HP and then used for modding (simply activating all settings, no other modifications on code!).
Is this constellation the same for both of you? Maybe the old bios version is the cuprit?