That would be nice, but I don't think it is possible for a jar file to have a customized icon.
I'm not closing the feature request though, because I want confirmation of that fact.
Now I'm confused, if only because the daily builds and the release builds are both jar files. I know that one of the places there is (was?) operating specific code in KoLmafia had something to do with the icon that was displayed on Windows when KoLmafia was minimized to the system tray. So while we wait for people to stand in line to order whatever it is that they think I have been smoking, why don't we step back and ask the OP a couple of questions, specifically,
What do you do to display the KoLmafia icon? Operating system? Where does it appear on the screen? Is it just there or do you do something like minimize to see it? Is there any chance that you have associated an icon at the operating system level?
What is different that makes you say it is present for Official builds but not the dailies?
I ask because, depending upon what the situation is, there may be a trivial fix to the build process that addresses it.