So I run a Powershell script from a bat file elevated and it mostly works great, however when it starts a job in the ps1 file it seems to fail. This script runs flawlessly if I run from an elevated powershell window manually. Any Ideas?
Not really, no. You'd need to somehow hardcode clear-text credentials, which would be pretty horrible. I imagine you could try running it as an Scheduled Task or something, which had alternate credentials applied.
I mean... not to put too fine a point on it, but what you're asking for would be every malware author's wet dream. You pretty much DO NOT want that capability in Windows :).