Sorry, I had missed one line in the JNLP which needs to be there for the warning to appear twice, as long as you do not check the checkbox to "always trust content from this publisher". That one line is the <property> tag, like:
<property name="test" value="test"/>
Also, the <security> tag asking for all-permissions is important for my app. If I delete any one of the three items (max-heap-size, the security tag, or the property tag), the signature warning only appears once. Thanks for looking into this issue, I appreciate it. And yes, I can reproduce the issue on another computer. I can provide the link to the actual JNLP and the app I use but because it requires all permissions I don't think anyone would want to run it, and so I just provide an example. The app that I am using for
testing is a very small one that does nothing other than display a frame.
So the whole JNLP is as follows: