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When I turn MIDI Clock IN on, it blinks.

I would say that the Pedal isn't getting midi Clock data from  you're Alesis

Agreed.  I first noticed this in one of the V3 updates.  The blinking indicates that the 'Factor pedal isn't seeing any MIDI clock input.  When it recognizes the timing pulse, the blinking stops immediately.

Does this indicate that I need to fix some other setting?

As imerkat says above, check the MIDI/OUTPUT value is set to THRU.  MIDI clock is transmitted over all MIDI channels, so you don't have to be concerned with that setting in this particular scenario.

You also need to check if the SR-18 is actually sending MIDI Clock (page 47 of the manual under Page 6 SEND CLOCK VALUE TO OTHER DEVICES (CLOCKOUT).

I also tried to make the Timefactor the master, and the Alesis SR-18 the slave, but that did not work either.

See the same page of the Alesis manual for CLOCK IN, and – on the TimeFactor – switch MIDI/OUTPUT to XMT.

Or, is both sides of a dual cable just like one separate MIDI cable?

If it's the type of cable that I'm visualizing (and not a MIDI "splitter" – which doesn't work), then it's just two regular MIDI cables seamed together for convenience.  Make sure that Alesis MIDI Out/Thru goes to TF MIDI IN, and vice versa (for using the TimeFactor as the master).  Sometimes it's an easy mistake to make.