I can't count the number of times I've been given or seen other people been given crap in Africa or Asia for not having an airline-printed boarding pass. Hell, even when I was flying CGK-SIN-HKG-EWR, with the first leg on Singapore Air, I got crap from United in Singapore for having a boarding pass that wasn't printed on United card stock (it was on Singapore Air card stock). They were able to quickly print out a boarding pass for me at the gate, so no issues thankfully.

In some third would countries, however, you can get screwed over like you did. In one case, this caused me extreme pain in Mumbai when connecting to a flight and I had to go through an exercise and a half when connecting. Basically I had to wait in a chair with no access to food/drinkable water for 3.5 hours before the airline check-in counter opened because they wouldn't let me connect with a printed BP that would be completely legal for me to board a flight with in USA.

Also, last week I flew back MPM-JNB-JFK and South African Air was holding people at the BP scanner in JNB who only had a printed BP.