Open the Site Manger, select the site, then select the Advanced tab
Change the option
resume support from
(auto detect) to
yes
I suspect the problem is caused by the reply number from REST which gives a false positive for resume support, setting the option above will skip this test.
You'll need to actually attempt to resume a file to determine if FlashFXP is actually compatible with this FTP server.
If it doesn't work you can download v4.0 RC1 from
https://oss.azurewebsites.net/download.php?s=4