Scheduled publications run for a long time

We are having severe scheduler problems. Every morning we have thousands of webi reports scheduled and a few hundred publications. The publications may contain 1 - 10 webi reports and the vast majority don't do anything special like bursting. They are mostly being used to have to schedule 'less' things by bundling the webi reports. One example i have is a publication contains 2 webi reports. Individually the reports run in minutes but as a publication it will take hours. These long running publications are causing our webi reports to be stuck in pending or take a longer time to be submitted.

Interestingly enough when i terminate and pause all publications in the morning, the webi reports flow through the scheduler. I can then resume the paused publications in the afternoon when activity is light and they fly through the scheduler.

Why is running them intertwined causing so many issues? We are on BI 4.1 SP5 if that helps.