The performance of jDOSBox is not nearly as good as that of DOSBox, but then its development is only about 3 or 4 months old. It also does not use SDL.
I'm not sure what's going on there with the screen flickering. I mean the cursor flicker is real bad in missile command of shoot em up because of the way I did my stars. But the screen... But if cpu speed is slower then I guess it could cause it, but it would only be guesses. I do notice though that kq2 play speed seems real close to normal whereas neither of mine are.
I have not noticed any screen flickering in the missile command part of shoot em up, but then I have not tried it on one of my older PCs. I also noticed one reason it takes the games to load. You have it set to download the unziped IMG files. If you drop them in a ZIP or a JAR they will only be 2-4KB in size instead of ~4MB of the IMG. Shoot em up weighs in at 289 KB compressed in a JAR.
To mounting an IMG from a JAR:
<applet code="jdos.gui.MainApplet" archive="jdosbox.jar,game.jar" width="640" height="400">
<param name="param1" value="imgmount c jar://game.img -size 512,16,2,512">
<param name="param2" value="c:">
<param name="param3" value="autorun">
</applet>
Just remember that the "game.img" needs to be in a "jdos" folder in the "game.jar".