Any difference b/w running exe manually and task scheduler

I have a console job for generting pdfs(to generate 10000 pdfs)

1. When executing through task scheduler I am facing error "window handle exception" after generating 1100 pdfs
2. When executing manually or from command prompt, job running successfully and generating 10000 pdfs.

Can any one suggest what may be the issue while running through task scheduler.

Suggest me any software to find any memory leaks, GC Collect, Windows Handles utilized.