Because this sequence may lead to breaking your working copy of FlowJo, we recommend not to do this. If you feel comfortable manipulating contents of jar files, read on.
1) Exit FlowJo. Locate the file, "FlowJo.jar".
On your PC: Program Files \ FlowJo Vx\ , or Program Files (x86) \ FlowJo Vx\.
On your Mac, it would be inside the flowjo Vx.app file (right-click, show package contents) in Resources / Java.
2) Open FlowJo.jar with an archive viewer that lets you access the files inside it. I use 7zip.
3) inside the jar file, replace /images/etc/chrome_startup.gif with another animated GIF. FlowJo doesn't care about the resolution or size, but those may be worth considering on slower computers.
4) save and put your modified FlowJo.jar back to where you found it in step 1.
next time FlowJo starts, it will use your animated gif instead! Notice that images/etc/ponies.gif was used in the 10.0x placeholder post, for example. Static GIF files can also be used. This was my favorite during beta testing: