First get all the information you've stored for your FTP accounts, because this will lose them until you re-create them.
In UE, go to Advanced->Configuration
Scroll down to the FTP section.
Click on FTP
Place a checkmark in the "Store FTP accounts and settings in user selected file"
Then enter a file and path, I entered:
Ok, now create a new FTP account:
Click on File->FTP/Telnet->FTP Account Manager
Enter the account info.
Enter the "Initial Directory" I entered:
Now this is important!
Click on "Apply"
You'll notice that the path is stored in HEX, something like:
Highlight and copy that line.
Now click on the "OK" button.
Shut down UE.
Using Windows Explorer, manuever to the directory where you setup the "user selected file." I used:
Double-click on the file. It should launch Notepad if you use the .txt extension. If not, choose Notepad to edit.
Scroll down to where you see the path you entered. On the line below it, you'll see the HEX data. It will look like:
Now paste the stuff you copied over the data assigned to "Initial Directory2." When done, it should look like:
Now save the file (File->Save or Ctrl+S).
Re-launch UE. If you check out the account info, you'll see it's stored correctly now and will work properly when you connect to the server.
If you edit the account, it will screw up your inital directory again.
If you have rights to your AppData directly, you can just edit the Uedit32.ini file: