Hi Chow, sorry for the delay in getting back to you.
We have investigated this issue, and it looks like you're setting some 'circular dependencies' with those checkboxes, where each checkbox depends on the other checkboxes, which is something that Geneious can't resolve and thus crashes.
We will try to improve this, the wrapper creator should not allow these circular dependencies in the first place.
In order to solve your issue, you'll have to remove the `pluginWrapper.xml` file (or modify it to remove all these <dependencies>) in order to start Geneious again, and then adjust the plugin.
I would suggest you use a 'Dropdown' option instead of checkboxes, similar to the screenshot below:
The two important settings here:
* Set the 'Name-Value Separator' option to Ignore the command line switch so that `ThisWillBeIgnored` will indeed be ignored
* Leave the Command Line Text for the default value `Fast (default)` empty