Having just gine through a similar problem myself (with much less equip.) Here are a few things to consider and/or look at
Do you have the proper pad size? It should be the same size as the pad on the BGA.
Is the board warping during your operation?
Where and how are you placing T/Cs.
What type of package are you working with? PBGA, CBGA, CCGA, etc...
Are you applying paste or just attaching with the balls?
My problem ended up being a combination of pad and PCB design along with a bad thermal ramp. Excessive ramp rates will cause the corners to bend "like tater chips" (this is a copyright infringement of a well known subscriber). what was happening to me was one side of the BGA was going into reflow long before the other side due to copper layout. With the oversized pads it would also allow the part to settle abnormally low and would also cause the part to move around during reflow. I had to apply a much longer preheat from the bottom side and reduce the temp on the top side until the package and board reached 170 C across the entire area. I then apllied just enough heat from the top to bring it up to 200 C. This fixed my problem.
P.S. for all of you that responded to my BGA rework thread "MUCH THANKS"
Oh yeah, I almost forgot: Search the archives for more info.
Russ
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