I assume you are using WinSCP package from PortableApps.com.
This is not supported here.

Note that WinSCP is portable on its own:
https://winscp.net/eng/docs/portable

So if you replace WinSCPPortable.exe with winscp.exe directly, or even better with winscp.com, it would work as you need.

Basically i have a batch script calling winscp and then manipulating the files(compression, parsing, copying, etc) once they are downloaded

The issue im running into is when i call my batch script, winscp seems to get executed into the background causing the remainder of the commands in the batch script to not work so well as not all files have been downloaded yet

The winscp call in my batch script is very simple and looks something like the following

<some batch script here>
folder\folder\WinSCPPortable.exe /script="winscp-script.txt"
<some batch script here>

Any ideas?