Hello,
I'm not quite sure why you would be unable to save a site profile password with application password protection enabled. I tested this several times by turning application password protection on and off and was unable to find any problems with using application password protection.
When you enable application password protection the data files are encrypted on write and decrypted on read. The internal data structures remain the same.
Are you storing the sites in your site manager or via quick connect?
I will continue to investigate this issue and see if I can find anything that might explain it.
What version of Windows are you using?
Are you using a standard or portable installation of FlashFXP?
Please verify to ensure that none of your data files are marked as read-only, you can find the data folder location from Help > About > Details tab.
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