Flight Path Problems/Behavior (disappearing)

I am very upset at how Flight Points now appear to work. I don't mind having to acquire them, but I don't want to have them taken away from me... I'm going into a lot of detail here as I want to be as specific as possible so I can get some clarification.

Recently I started a character on Sargeras - which is a PVP server. As my first character there, I have no BOAs, or friends with two person mounts to fly me around. That means like many "beginning" players, I have to acquire my flight points the hard way, by riding the distance and picking them up.

On about 6/24/13, I didn't feel like questing. I had primarily been questing in the Eastern Kingdom, so I decided to fly to head to Kalimodor and pick up flight points there. I "ran" all the way from Darkshore to Feralas, picking up several flight points including the one in Karum's Glade in Desolace and a few in Feralas. I then did the quest in Feralas to take the boat to the barge in Thousand Needles. I picked up the quest and flight point on the barge and hearthed home thinking to quest the next day.

On 6/25/13 a friend offered to run me in some dungeons in Eastern Kingdom. I took the rocket from Lights Hope Cathedral to Fuselight and then ran all the way across the Badlands AND Searing Gorge. I picked up several flight points along the way.

Afterwards, we decided to go to Kalimdor to run ZF. When I arrived in Darnassus I found the flight points for the Barge in Thousand Needles and Karnum's Glade were missing. The Feralas ones were showing. My friend and I flew to Feralas and ran all the way to the Barge, where it showed I COULD NOT pick up the flight point. We then ran on to Tanaris and I picked up the flight point in Gadgetzan (getting ganked several times in the process). We ran ZF and I hearthed home.

On 6/26/13 I found I was still missing ALL of the above flight points. I filed a GM request and was told it might be my addons and cache. I tried the recommended procedure and the flight points STILL did not appear. However, that request came many hours after I wanted to play, so once more I took the long run (not knowing the shortcuts) across the Badlands - checking the flight points as I went. I could not pick any of them up, yet I could not see them when I wanted to fly. I started questing in Searing Gorge, and lo and behold, ALL of the flight points in Badlands AND Searing Gorge suddenly appeared!

On 6/27/13 I decided I wanted to do the Silithus quests instead of Blasted Lands. I took a portal to Darnassus and I was once again missing the flight points to the Barge in Thousand Needles and Gadgetzan! Once again, I flew to Feralas and took the long trek to Gadgetzan (where i couldn't pick up the flight point as I already had it). I cut across Tanaras, UnGoro Crater, and finally into Silithus. When I got to Silithus, I checked the flight points again. The missing flight points were not showing up. I did several quests and checked again. BINGO!!! Flight points were now showing.

It now appears that you MUST quest in an area before the Flight Point is going to show up. I would like this confirmed. I am VERY unhappy about this. I prefer to do my "running" to pick up flight points at the end of questing when I am tired and don't feel like doing anything complex. This forced me to waste hours of my time. The GM who responded to me did not mention any ties between flight points and questing. He blamed the problems on an addon - which I did not have active for testing.

Again, in closing, could we please have some clarification of how flight points are now acquired permanently AND why they disappear?