My question now is, will this be resolved with a firewire connection? I.e. should I buy the optional FW16E FireWire Expansion to add functionality of automatically reconnect midi? If yes, I consider so because it will enhance my workflow. (I don't need the audio multi channel funtionality though.)

No, do not get the FW16E if you don't need the "audio multi channel functionality".

To resolve your issue, power on your gear, then power on your computer. Launch your DAW software last. While the DAW launches it surveys what is connected to the computer. It actively checks the computers ports, it should find all of your connected hardware and establish connections.

By turning off your gear, but not the computer... "... disconnecting power of all hardware except for the pc." You break the knowledge the computer has of these devices. You need to allow your computer to rescan it ports.

Although you don't mention turning the computer OFF, we are going to assume you let it "sleep" or "hibernate". This action is causing your computer to "forget" what is connected. I'm no Windows expert but if you are saving energy by powering down everything but the computer, instead of just waking the computer - power on the rest of your gear and then reboot the computer.

Windows will fully reawaken when you reboot. If not, you will continue to have it baffled by not finding the ports. Avoid SLEEP and HIBERNATE.

Reboot!

Thanks for the quick response!
Yes, I know rebooting the pc reconnects everything, this functions ok. But it takes a while and it's not so handy for me, to first reboot the pc, then reboot Cubase and then re-load the project.
I was hoping with firewire, reconnecting the Mortif rack xs would function like my Steinberg/Yamaha MR816x audio interface, which automatically reconnects after switching his power on again. But I guess for midi this is not possible?
(I don't put the pc in sleep mode, I keep it on, but power down monitor and gear.)
Thanks,
Anthonie de Boer

I don't profess to be a Windows 8.1 guru, but there probably is a way to have your computer refresh its scan of connected hardware without rebooting. I wouldn't blame this issue on the type of connector carrying the signals. And while I often do recommend the FW16E but only in a situation where it will fulfill an audio routing need. Not for your issue.

If I were you I'd exhaust the search for refreshing the scan before buying something additional.
If your computer has multiple users, try logging out and back in; that might refresh the scan, and would certainly be quicker than a full reboot.

Let us know.

Thanks for preventing me from buying something I don't need.
It seems to me the issue is caused in Cubase rather than in Windows.
If I close Cubase, then switch off and (after the break) on the Motif rack and then restart Cubase, everything functions ok.
The disadvantage of this method is: it can take long to restart Cubase and reload a project, depending on the size of the project.
(Eventually rebooting Windows 8.1 is not the problem, that doesn't take long on SSD drive. By the way, my computer does not have multiple users.)
If I turn my gear off but DON'T close Cubase, after powering on, all my midi gear except for the Motif rack again is connected via my midi interfaces (Steinberg Midex8 and Motu Midi Express128) because these are usb-bus powered from the pc. Also, my Steinberg/Yamaha MR816x audio interface reconnects after a very short moment.
I did this experiment: I dis- and reconnect physically all midi, while Cubase stays active. Now the Midi Express is again functioning while Midex and Motif rack have lost connection. After closing and restarting Cubase, the Midex is again functioning while the Motif isn't. The only way to get the Motif functioning again is to reboot the pc.
Now I have a few workarounds, with each its disadvantage:
1. When I take a break, I can close Cubase and when continuing, after repowering the gear, restart Cubase and reload the project. Disadvantage is, it takes long with bigger projects.
2. I can put the Motif rack in MIDI-mode instead of USB-mode, and connect it with midi cable to one of the midi interfaces. Disadvantage is, I can't use the Editor.
3. I can leave everything powered on (or connect the Motif rack to a separate powersupply and leave that on). Disadvantage is wasting energy.

Still, for me, it's not obvious that a firewire connection won't reconnect while Cubase is staying active, taking into account that it uses a different driver than the usb connection, and my Midi Express and MR816x audio interface DO reconnect.
I guess it's a simple experiment for someone with a Motif-Cubase setup with firewire, to turn off and on the Motif and checking if midi is still functioning? (after switching to "online" in the editor?)
Thanks,
Anthonie de Boer

I did some research on the Cubase forum. A rescan for midi ports in Cubase on Windows seems to be a feature request for a long time already.
http://www.steinberg.net/forums/viewtopic.php?f=19&t=20518
Sometimes reset MIDI Port Setup in Devices in Device setup seems to do the job for some devices but not for me now.
I guess it's gonna be trial and error with the firewire connection. I consider ordering the expansion and send it back when it don't work. Unless it's for sure it's not gonna function anyway?