Yil: Heres something you can reproduce, it has to do with No_SubDir_Sizing = True
New install of ioftpd, I just simply changed host / port and enabled No subdir sizing and Hide_Xfer_Host in ioftpd.ini
my root looks like this
/
/test
/test/test1
/test/test2
try uploading a file "crap.txt" with some text in it, inside /test/, both test1/test2 will disappear from the dir. If you remove the crap.txt file, both folders appear again.
disabling No_SubDir_Sizing fixes all this, but I hope it can help you in some way of finding the error
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