What version of Windows are you using?
Which windows theme are you using?
What version of FlashFXP are you using?
I am unable to reproduce the problem with the button clipping, I suspect that it is related to the windows theme, or it might be an issue specific to the version of FlashFXP you're using. I'll know more once you provide the answers to the questions above.
To turn off the welcome message popup
From within FlashFXP on the main menu select Options > Preferences, Then from the Preferences dialog, General > Options and uncheck "Pop up window for login messages"
To clear the saved SSH Host Key you need to open the flashfxp.ini in notepad and manually remove the saved entry.
You can locate your FlashFXP.ini from within FlashFXP from the main menu Select Help > About, then from the About dialog select the details tab. The FlashFXP.ini is stored in the path shown under "Data Folder"
The SSH Host Key is stored under the [SshHostKeys] section.
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