Thank you very much for the swift reply. Indeed we have quite a lot of plug-ins that load when rhino starts, as for instance auxpecker, rhino gold, rhino jewel, t-splines etc. Deactivating some of them on start up has radically increased the start up time. The files are all saved normally. However, generating viewports does take quite a long time. And no, it does not take 2 minutes every time, the start-up time is related to the file size. Nonetheless the files take a lot longer to load than they would with rhino 4.
In any case, you helped a lot. Thank you.