I did follow the Wiki when setting up substreams and just reviewed again. Everything seems to be in order...Other than I have my main stream set to 2 FPS and sub set to 4. Setting the main to 4 helps a little but does not completely resolve the issue.@VirtualCam
Can you screenshot your Blue Iris Status window with the Cameras tab selected? Experienced eyes can find a lot of potential problems just looking at that.
It sounds like you maybe did not set up the sub streams according to best practices, and maybe something you did is causing BI to struggle with the main streams. There is a guide I wrote on setting up sub streams: Sub Stream Guide
Also based on what you say about the service shutdown time, I suggest you monitor the memory usage in Windows' task manager. See if it goes up over time. A number of things have caused Blue Iris memory leaks before, most notably Intel Hardware acceleration. Since you're running in a VM you should have hardware acceleration disabled anyway, but it is a common error for people to turn it on when it isn't actually available and there can be side-effects...
Not sure what is wrong
Hardware acceleration is off at the global level. It was off on most cameras and a few were set to default. They are all off now. Setting them all to off did not resolve the issue.