I have managed to reproduce the issue with "Undo" in the internal editor but I am unable to reproduce the problem with the disappearing icon in the system tray.
Can you please do the following
Locate the FlashFXP.exe on your computer
right-click and select properties from the menu
then click on the Digital Signature tab
Now click on the details button
What is the signing time of the signature?
It should be something like "Saturday, March 21, 2015 08:22:54 PM"
If its older than that then you may have accidentally got an earlier release of build 3820, we're having problems with MaxCDN failing to purge the cache of stale content.
If you've got an older release or unsure you can download the correct exe from this temporary
link (bypassing the cdn)