I have a copy of the CANFORGEN on this issue at work (I was going to laminate it and carry it around to show people who have taken the meaning and changed it to suit their own personal interpretation, usually to the detriment of the CF), and if I can find it here at home I will post it.
There is a somewhat sound logic behind it: that the current issue boots (Mk III) are not designed for running (poor arch support, nonexistent cushioning, generally poison tread pattern, esp compared to what is available in civvy market), so there is some merit in saying that troops shouldn't be running greats distances (particularly on asphalt or concrete) all the time, but they seem to have removed any grey area (and common sense, IMO) and said "no running in combat boots".
Personally, I still run the 13 km in the boots, and will take my lumps if/when I get busted, and I have had to "counsel" young/keen soldiers, who want to run along with me, that they are on their own if they get hurt. Nice system, where keen soldiers can get punished for wanting to "be all they can be".
I don't know how long this policy will stay in effect, as I doubt there are any plans to get rid of the Mk III, so the steady decline in overall fitness of soldiers will probably continue [Note: edited for use of double negative.... Al]
Al