Application startup on a server can be slow, but an hour is ludicrous.
If server has internet connection, my first guess would be a trojan, or other adware resource hog. Straight AV software is not likely to detect this. Suggest try Adware, or Spybot, free downloads to check this. Also HijackThis, but you will need help to analyse results, there are web sites where you can have this done.
If not on internet, may just be that you are overloading server. You have not given details of Configuration, or software installed without which you will not get much help.
Two things to try though :
1) Try changing setting in performance options (System) to give priority to applications rather than services, not normally a good idea, but will make it easier for you to investigate problem.
2) Try swithing off some services, to see which are causing problems. Task manager should give you some idea of where the problem lies. Could be all you need is some more memory, still quite cheap, even for Proliant.