One thing to becareful of is missing part of the column when doing the cleanup.
I have seen this myself on both our 3100 and 3700. Sometimes loading hte column
too fast will cause some sample to run down the side without gong through the
column. We stopped using the G50 columns as they didn't work as well (we saw
more blobs and weaker signal) so we switched to the Qiagen Dye-Ex removal 96
well plates. they work very well for us. The one thing we have noticed is that
you have to wash them after you remove the buffer before loading the samples.
WE run 200 ul of water through then load the samples. WE are getting much
brighter signals with the BD v3.0 since we started washing the wells.
Director DNA Sequencing Core Facility at Caltech (former ABI service engineer)