When I save my bubble plot as Adobe flash and open in browser it plays the timeline but there are no bubbles visible on the plot. The jrp works fine.
Yes, please do report the issue and include JMP version, browser version, and flash plug-in version.
If you are using JMP 12 or newer, you might consider using the Interactive HTML5 version (File > Save As > Interactive HTML with Data). HTML5 is where recent development has focused, and in JMP 13 HTML5 will support the new frequency role in Bubble Plot.