The 1.1 software is a bit buggy but at least in our hands not any more than 1.0. The bugs are different though. The spatial calibration always gives an error message whenever you run it. However, this doesn't seem to effect the data quality.
If you are doing genotyping, you really have to use the 1.1 software. The 1.0 software had major problems with matrix bleed-through. The 1.1 software is better at the matrix correction for genescan. One caveat is that the signal strength using 1.1 is reported to be 2/3 of the signal stength of 1.0. I don't know if this has something to do with the improved matrix correction or not.
Robert B. Chadwick
Director, Genotyping/Sequencing Unit
Division of Human Cancer Genetics
Ohio State University
420 West 12th Avenue
Columbus, OH 43210
phone (614) 688-4783
FAX (614) 688-4761
e-mail chadwick-1 at medctr.osu.edu
web address http://gsu.med.ohio-state.edu/