My current game is...
..fully patched
..playing the "All NPC'S at the Beginning" mod

I started with a full party and worked my way to the Friendly Arm. Talked to Jaheira and chose the 'go my own way' option. We went and did some of the quests around the FAI and returned and sold loot. Jaheira and Khalid were still there(pretty sure). We went South to do the Nashkel mines and various other southern quests. Thru party attrition[digression..I play that when a party member is 'chunkified',,THEN they are truly dead, and you are out of the party] we went back North to get Quayle(found in the FA in this mod) and noticed that Jaheira and Khalid were gone. I wouldn't think this would be caused by the mod,,because J&K are found in the same place in both mods. Any body seen this before? Bug?

I had the same problem!!!!!

was playing with all patches + baldurdash but without any mods. left j&k in FAI. when i reached baldurs gate city, i one time went back to get them. they were gone. thought it a very strange bug then. now i see someone else has it too.

I don't think its a bug... it might be, but would *you* like to sit in the FAI for months? years even?

Khalid & Jaheira have a quest: Go to Nashkel and investigate the problem(s) in the mine.

Once you clear out the mine and start Chapter 3, J&K have no reason to hang around anymore, and move on to other things.

Yep. You gotta have the Dynamic Duo Of Marriage in your party before Nashkell, otherwise they skip town (or the FAI anyway).