This repository reproduces a bug found in sbt-native-packager, specifically with how javaOptions are set when using the plugin JavaServerAppPackaging. The bug can be observed by loading SBT Shell (I was using version 1.9.9) and running the command show javaOptions. You will observe the following output:

[IJ]show javaOptions
[info] module2-nojavaoptions / Universal / javaOptions
[info] 	List()
[info] module1 / javaOptions
[info] 	List(-Dsome-property=true)
[info] module3 / javaOptions
[info] 	List(-Dsome-property=true)
[info] javaOptions
[info] 	List(-Dsome-property=true)

Note that module2-nojavaoptions has no javaOptions set, where as all other modules do. In particular, module3 has the same definition as module2-nojavaoptions, except for we append an empty sequence to javaOptions, which seems to make the module once again see the javaOption being set.