Another problem they never mention are artifacts from the chemical protocol; just the other day we found a very unusual anomaly that indicated the first 1/3 of all our reads was absolutely crap (usually only the last few bases are unreliable); turned out our slight modification of the Illumina protocol to tailor it to studying epigenomic effects had quite large effects of the sequencing reactions later on.

Do you have any more details about this? I'm working on solexa sequencing of ChIP DNA with (modified) histone and transcription factor targets. These runs are expensive so it would be nice to avoid problems that someone else has already gone through.