You should not rely in your GUI configuration file in your scripts:
https://winscp.net/eng/docs/scripting#configuration

If you need to, for some historical reasons, set the INI file read-only, so that the scripts won't try writing to it.
https://winscp.net/eng/docs/config#ini_readonly

i am running winscp via SSIS jobs. i have several jobs that execute together at the same time....90% of the time it works fine but in the other 10%, it just so happenx that two winscp transfer are attempted at the same time.

I was under the impression that it should run fine together but that doesn't appear to be the case for me. I get this error for the second job that fails:
Script: Cannot open file "C:\Program Files (x86)\WinSCP\WinSCP.ini". The process cannot access the file because it is being used by another process

The error doesn't appear to be the executable but rather the configuration file.

Am running 5.5.5 build 4605.

Do I need to update, Is there a workaround I can for this or is it a limitation of winscp?

Thanks!