If you saw any speed increase after rebooting and running permission fix, it's probably caused by the reboot, not by the permission fix. Believe it or not, OS do leak memory, and over time you might feel the computer getting sluggish which can often be remedied by rebooting. Permission fix is just that, fixing file permissions on the disk.
Cron is a software that can run some specified task every some interval. Like you mentioned, cron can be used to rotate old logs. You can use cron to remove temporary files in regular basis. You can run cron even to fix file permissions in regular basis if you wanted to.
Lastly, back to the original question. Taking a minute or two running excel seems plain wrong. I can only speculate without knowing details. One possibility is that the memory on her laptop is inadequate for Microsoft Excel software. I think you mentioned she had 380MB of memory. In my experience, Mac applications take up about 1.5 to 2x the space of comparable Windows apps. Windows laptop with 380MB or 512MB is plenty enough to do almost anything. On the other hand, Mac with less than 512MB of memory usually suffer from inadequate memory. One symptom that happens when the machine is out of memory is it starts dumping memory content to the disk, called swapping. When that happens the system slows down a lot, causing a simple task for a minute or two to complete.
There is a tool that comes with Panther that's very useful for diagnosing this kind of problem. It's called Activity Monitor, and it's in utilities section. Fire it up, run the Excel calculation and take a look at these three sections: CPU, memory, disk. I would look at the memory section first. If you don't see any free memory or very little free memory left, you need to get more memory to your system. In the disk section, see if you notice any disk reads and writes reported there. Excel calculation is purely CPU bound, and should involve little disk access. If you see some sizable disk activities, her machine may be suffering from swapping, resulting from not enough memory.
As for your newly added memory, if the system reports it, then it is being used. You should be able to see the increase in the Activity monitor memory section.