The problem arises from the fact that FlashFXP uses MLSD by default and ProFTPD by default doesn't display symbolic links as folders when using the MLSD command.
A configuration option was added to proftpd to work-around the issue but to the best of my knowledge this is not turned on by default.
The following must be added to the proftpd.conf if it doesn't already exist.
Code:
ShowSymlinks on
<IfModule mod_facts.c>
FactsOptions UseSlink
</IfModule>
Additional information regarding this issue can be found on the proftpd.org website
http://bugs.proftpd.org/show_bug.cgi?id=3747
If you do not have root access to the server to change the configuration, there is one other option and that is to force the
List Command in FlashFXP from within the
Site Manager > site profile > options
Change the List Command from auto detect to LIST
The MLSD command is far superior to the original LIST command and that is why we use MLSD over LIST by default whenever possible.