Okay thanks.
I'll continue testing this to/from different sites and with different settings to see if I can get it to work like it should or have 100% sure way of reproducing the odd behaviour. Maybe it's related to a site-specific setting in Site Manager, something I haven't looked into yet.
EDIT: Okay this didn't take long
I checked the Site Manager and saw that I had used the "Use site ip for passive mode connections" option for the source sites. After I disabled/unclicked that option this A -> B -> C queue thing works for me too!
Exactly what does the "Use site ip..." option do and in what way would it affect transfers? Would it change the behaviour in such way that FlashFXP does not refresh the source dir?
Hope you can reproduce it now.
EDIT #2: Guess I spoke too soon
Still no list on site B before transfer to C starts. Must be the way I'm queueing the dir that is wrong, or that I just click "Go" after I've queued it. Maybe I have to refresh once manually either inside the dir on B or in parent dir. I dunno.
I'm ready to give up now