The latest version of Safari causes issues when downloading files such as your IRD returns. While the file will download, doing so now causes the Flash player to freeze which will stop FlexiTime from working. To continue to use FlexiTime after downloading a file it is necessary to quit Safari (by right clicking on the Safari icon in the Dock along the bottom of your screen) and restart.
The issue is limited to Safari. Other browsers such as Chrome do not have the same problem.
A fix is under development by Adobe. It looks like this will be available in either the November or December release of the Flash player.