I'm having the exact same problem. The Quick Connect History is cleaned after i quit an instance of ffxp. This is with beta 970 even. I was using this a lot but ever since i upgraded to 2.x it's kinda M.I.A.
Is there something i'm missing in the ini ? Cause i cant find any settings that would clear it and it's not in de FAQ either.
*nevermind* fixed it already
Deleted the quick.dat and let ffxp make a new one. It's working now.