scripts adding new fileformats or colourschemes do not work when run via command line

Some groovy scripts (colourscheme registrations) appear to be ignored when run from command line. Originally reported as JAL-4305, this bug now covers specific problems with the following groovy scripts in examples/groovy:

colourConserved.groovy
colourSchemes.groovy
colourUnconserved.groovy
fileFormat.groovy

These work when run in the Groovy console, and a new alignment window is opened, but when run from the command line using either old -groovy or new --groovy, the registered colour scheme(s) and file formats do not appear in new alignment windows.