There is an extensive discussion of Married Segment Control on Flyer Talk and it seems what MSC entails is as 'fluid" (and confusing) as some people's idea of what gender is. Firstly, there is the perception that MSC only applies to award fares when airlines do also regularly use them for revenue fares as a form of maximising profits. The classic married segment situation for award availability (i.e. the one which is easiest to understand) is when you can only book 2 segments as a pair i.e. you can't book one or both of the segments individually but they are readily available if you book both together......... The time it might differ is when married segments are involved... so you'd see availability for two flights together, but can't break them up (for example TPE-HKG-LAX might be available, but you can't book the HKG-LAX by itself).........
The converse of that is exemplified by how CX applies MSC to awards on their flights through their hub of HKG. In this situation CX will, in many instances (particularly Aus - HKG - Europe), not allow you to transit HKG on two CX award flights. The "go-round" for this is to either stay more than 24 hrs in HKG or replace one leg with another carrier. If, say, you wanted MEL - HKG - JNB, CX won't ticket it if both flights are with them but if you book QF from MEL - HKG and then CX from HKG you won't have any problems at all (assuming there's availability on both flights, of course).
Edit: If putting together a OWA itinerary online and you see CX J availability for connecting flights such as the example above, you will almost certainly be able to "book" them as part of a multi-city itinerary and receive an Itinerary Receipt from QF (without an eTicket number), but in fact this itinerary hasn't been properly ticketed at all at that stage. Sometime over the next 24hrs those two CX flights will just vanish from your booking because CX won't ratify them.