Ok, more interesting information regarding this issue:
1. Used the Query widget, and the point is recognized, and the associated popup works when I hover over the point in the results table. I can even zoom into the point correctly. A little limited on what you can write in the results table (no html?). But all seems to work correctly using the query widget, and display results popup.
2. Also used the search widget, I can draw a box around the spot I know contains the point on the map, but the results table puts the point back off the coast of Africa again. Although it locates it correctly point wise, just not popup wise again.
I am pretty sure it is a bug with Flex, not my layer. See attached image that has both widgets being used on these points.
[ATTACH=CONFIG]11935[/ATTACH]