Instead of adding pci=nomsi (which did not fix the samba issue and disabled all usb ports on my haswell box!)
Try adding pcie_aspm.policy=performance instead.
Thanks go to Matt Devo on the Kodi forum for this tip..
Updating to one of the latest builds from Millhouse
fixed the video calibration saving issue for me on my Haswell based machine, settings now save and survive a reboot.
I have a similar issue with slow SMB (Samba) browsing and random buffering issues since 9.0/9.01 on my 2 Intel HP Haswell based machines.(No Windows SMB shares, just between to Libreelec machines on a gigabit wired network)
Accessing the same files and folders via UPNP shares works perfectly however with fast browsing and zero buffering, this problematic SMB behaviour was not present in previous Libreelec releases I have been using.
I believe there is a kernel 4.19 regression issue which affects Ethernet performance on Haswell based machines (info via Chromebox - Official Kodi Wiki )
I applied the fix suggested but this did not solve my SMB issues
Using UPNP to share files is a workaround that works for me now but hopefully this SMB problem can be tracked down and fixed as otherwise the 9.01 release is running great.