This is a mystery I am detecting in my setup as I configure my system. Cubase is registering a pulse in the the midi in and out activity meter in the transport panel. The obvious solution would be the click is on, or a metronome, but that isn’t the case. The pulse continues even when I turn off my synth module. I haven’t been able to get audio working yet, but the pulse, as I say is registering loud and clear as a visual. Any ideas as to where I might search?
How rapid is the “pulse”? Could it be reading some external MIDI clock, or an external MIDI source that generates “Running Status”?
The pulse is 52 bpm. Yes, maybe it is reading an external clock, but I’m in the middle of setting up my system (still waiting for another saffire Pro40 and cables to make the clock settings. Maybe I’ll be able to find out if I set the saffire to internal clock. Don’t remember. Thanks.
Start unplugging your midi devices until the flashing stops. Now you can reconnect it again, and learn to live with it.
Well, I turned off all the midi gear to no avail. I didn’t unplug. Does that make a difference?
I had a very similar situation 2 yrs ago but ultimately isolated it to ac line noise. Used a separate source for the computer/interface and it went away immediately. Hope you find this … My 2 cents
Have we got the following facts right?..
You are seeing both the MIDI In and MIDI Out indicators flashing on the Transport Bar?
Are they flashing in sync with one another?
Is this happening even when Cubase is in Stop mode?
Maybe we need some more details on your equipment (PC or Mac, MIDI and audio interface, what MIDI devices connected etc.)
Does this happen even with a new, empty project?
When you record-enable a MIDI track, do you see the flashing there too?
Yes, try unplugging.
EDIT: Ah, I see an interesting comment from knuckle47… certainly try that too 
The Steinberg CMC controllers, send out a keep alive pulse, but I have seen keyboards do the same. Usually nothing that can be disabled, just a little annoying.
The pulse shows in both midi in and out (but sometimes, just out) in the transport bar and in tracks that are using VST (Halion), not on tracks that are using Motif hardware synth. They are in synch and approximately, by my count 48-49 bpm which is my time clock rate. I have unplugged my keyboard, my synth module. Still happens. Working with the Focusrite people, I used MIDI Monitor and got this message “Note on C-2 127”. This was repeated in the intervals that would be consistent with the identified pulse rate. Any thoughts?
Just to put a cap on this issue in case someone else has this maddening little problem. I will tell you that I have TWO of the Saffire Pro40’s. There is a manual for using two of these devices that is put out by Focusrite and in it it is explained that SPDIF cables have to connect the 2 pro40’s together (In to Out, Out to In). Doing this eliminated the problem. Connecting the cables/restarting the system/problem gone. Sorry to waste your time, but one can only read so many manuals at once. Pretty much, all of this gear is new to me. Thanks for all of your help.