The system fan is managed by the system BIOS in the system and may also be managed by operating system's power savings features.
In this case, there might be a conflict between your system BIOS and the operating system settings.
You should check directly with your system manufacturer to troubleshoot on this issue and replace the fan if its necessary.
you say your fan does not come back on after startup? if not does it overheat and turnoff ?i mean turn computer off? mine is a acer but mine has a way to turn on fan manually, you have the manual that came with it?.