I have a similar problem. I installed the new version 2 (r11710) win64, and tried to open a v2 pipeline from a colleague.
The header of the Pipeline file is:
CellProfiler Pipeline: cellprofiler.org
It keeps giving me the error:
"Pipeline file version is 2. CellProfiler can only read version 1 or less. Please upgrade to the latest version of CellProfiler...."
has this issue being resolved?