Sometimes you need to completely reset FlowJo. Uninstalling the program isn't enough...you also need to delete the preference files. Resetting to factory default just isn't enough.
Now, this doesn't happen very often, and make sure you know your serial number (if you use one) before you do this (because you'll have to re-enter it), but to find the v10 preference files, pathways are below:
for Windows- C:/Users/yourAcct/AppData/Roaming/FlowJo10/flowjo10.prefsfor MacOSX-/Users/yourAcct/Library/Preferences/flowjo10.prefs