Yes, i am able to set both lights to flash in the following modes: Auto, High Visibility, Night and Trail modes. When in a Network I can set both lights to flash in the same mode.
One thing of note is that the rear red light, the Flare RT, has a built in ambient light sensor. When this sensor is on, it overrides the flash mode you set when it there is low light (i.e. indoors). I figured this out after noticing that when I set the flash mode of the Flare RT that it would start flashing to the mode I set it, but then after a few seconds go into a steady, lower light mode. Play around with it and you'll see what I mean. The ambient light sensor can be turned off completely to avoid this problem - download the manual to see how to do it.
No problem, I'm glad to know that my problem wasn't isolated and that I was the only one with this problem. Other than this light network problem, the form factor, battery life and visibility of these little lights are fantastic!