I just tried new version 0.12.0 was using 0.11.6 The user interface has some flashing issues with water tiles and If I open some dialogs, no way to close them. I'm on windows 10 on a 5 or 6 year old laptop. I tried turning off some options under display with no better results. And the dialogs that wouldn't close didn't have a close button of any kind.
When you say flashing issues: Are you seeing the tiles as black?
If yes, this might be caused by an OutOfMemoryError caused by running the game using old startup scripts. In that case, please reinstall FreeCol using this installer:
https://sourceforge.net/projects/freecol/files/freecol/freecol-0.12.0/freecol-0.12.0-with-java.exe/download
Please attach one (or more) screenshots to illustrate the effect if the flashing issue is something else.
Can you please attach the file "FreeCol.log" to this bug report?