Vista - Missing files and folders in certain circumstances...

I have Vista Ultimate installed on my pc at home. I am a web developer and
sometimes when I'm using an FTP program (this problem happens with whatever
ftp program I use) I have a need to create a new folder. So when this
happens I usually just create the folder from within the FTP program because
the ones I've used provide that option. However, whenever I do that, if I
then bring up windows file explorer, it will not see that folder I just
created in the ftp program. Even if I reboot. In fact, I can and have from
within windows file explorer recreated the folder I had just created via the
ftp program.

Now, this happens with files as well. I've learned that if I need to create
a new folder I should create it via windows file explorer first. However, no
matter what ftp program I use, once I transfer files to that new folder (or
any folder for that matter), windows file explorer does not see these files.
As far as it is concerned the files do not exist. If I go into my IDE that I
use for web development I can see the files and/or folders just fine but
windows file explorer does not.

I hope someone has an answer for me on this because it is extremely annoying
and provides some challenges that makes my job that much harder to accomplish.

Thanks