Try using the Automatic (Delayed Start) option. That is what my test environment is set to, as my organization is in the process of upgrading to v10.1 (Large enterprise environment with tentacles into numerous non-GIS applications so upgrades are long and complicated).
No guarantee that this will solve the issue, but I believe this is the default value as I do not remember modifying this variable after installing AGS v10.1. I'm thinking that ESRI set this up purposely to be for a delayed start, as it takes time to wake up components of AGS.
Also, how often do you need to reboot your GIS server? I ask because I rarely have the need to reboot my production ArcGIS Server server (maybe once every 3-4 months). I also have my license manager on a separate server from my ArcGIS Server server, if its the License Manager that requires you to reboot your GIS server often.