Remember the following MCA appearance settings between different UGENE launches:
- Show/hide offset
- Show/hide chromatograms
- Show/hide overview
- Height of chromatogram peaks
- Consensus type and threshold
In case several MCA windows are opened, take into account the last set value.
Also, make sure all set parameters do not interfere with similar parameters in the Alignment Editor, i.e. values of parameters are limited to MCA views only.