The JCMT OT currently has a number of known bugs:
There are various problems when running the OT with the OpenJDK distribution of Java. Please use Oracle's version for the time being.
Many input boxes only "listen" for key-presses and don't notice other forms of input. For example if you paste text into a note, the text may not be stored until you edit it slightly.
Some input boxes are initially displayed at too small a size to allow their contents to be read. Adjusting the size of the OT window may cause it to lay out the boxes again.
The target information panel can mangle offset coordinates when the coordinate system is changed. Please double-check coordinates after changing coordinate system.