We have released a minor update for Auto PeakTrace that fixes a problem with skip short traces when trace trimming is enabled. It is recommend that anyone running Auto PeakTrace 5.61 upgrade to this version. You will also need to upgrade to the latest version of the CodeMeter runtime (5.20b) to use this version.
Auto PeakTrace 5.61 is available on Nucleics downloads page and will be added to the automatic update shortly.