I appreciate your suggestion to look into the machine but since the problem is apparently not related to the machine as such I have little hope here. The difference in performance is observed on a single virtualized machine in both cases.
I am using the virtual machine and log onto it by remote desktop. Performance for the script is fine when started from the console. The same script on the very same machine (me still logged on) is extremely slow when running scheduled. I have full admin rights on the machine and there is no indication that resources are utilized in a noticeable way when the problem occurs.
Re^2: Script slow only when run as scheduled tasks on Windows Server
In our case we saw what you are seeing, no indication that the resources are being being taxed at all. I suspect our problem was based in the virtualisation setup, not the windows setup. However as you say, if performance is normal when run from the console this isn't your issue. Perhaps it would be wise to profile your program running from both the command line, and as a service. Comparing the output should narrow down where the performance bottle neck is occuring. See Devel::NYTProf. IIRC Windows has an optimisation setting, which allows you to choose 'Programs' or 'Background Services'. This may also be worth investigating. 'System properties' -> 'Advanced'->'Performance'.