Are you using an Anti-Virus software, if yes which are you using?
We are aware of a issue with "InoculateIT PE" or "eTrust EZ Antivirus" that prevents FlashFXP from starting up, or results in a very long delay before startup. I personally contacted them and they recommended the following.
Thanks for your email. eTrust EZ Antivirus can cause these sorts of problems if the 'scan all files' and 'Closing files' option is turned on. This option should only be used in an emergency when a virus cannot be contained.
In most cases you will never have to use this option. To check for this option and turn it off open eTrust EZ Antivirus select 'options' then ''Real-Time-Protection'. Now select 'File Monitoring' and un-tick the 'scan all files' and 'Closing files' option. You will have to reboot your machine.
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