That sounds dicey, brah.
Unless you were using smaller than 20ga. wire, it's not the whole problem.

Grab you meter and measure across each emitter.
It sounds like the regulator is dropping out for lack of headroom.
That 48V. rating on the regulator is the maximum voltage, not the operating voltage.
It needs a couple volts of headroom to do it's thing.

You are asking it to regulate current without giving it enough "wiggle-room" do so.
And, the voltage drop across the junctions will creep as your emitters "burn in" for the first few months.
It's only a tiny amount but it is multiplied by the number of emitters.

LEDs are non-linear devices.
A very small change in juction voltage creates a relatively large change in current, yah?
So, this will get worse with time.
If you operate this puppy on the ragged edge of functionality, you are "standing into danger".:microwave:

Since these are current regulators, there's a simple test as well.
With the original supply cable, and the unit mis-functioning, just turn it off and clip a jumper across one emitter.
If she comes right back on line through several on-off cycles you have identified the problem.
You will need to get a third regulator and add that 5th led to a new string of reds.
If it were mine I'd do 4 X 625nm. for 36V.
And a new string for 4 X 660nm. for 42 V.
The regulators will then be re liable and will last a heck of a lot longer too.

Bottom line for good design?
Run cool and leave plenty headroom.

Aloha,
Weeze