I just noticed that with some islamic prayer time applets (but not mine, kprayertime ;-)), they have default location settings that include a non-zero altitude.

For the calculation of prayer times the important figure here is the altitude relative to the local horizon. This influences the time of sunrise (shuruuq, شروق) and sunset (ghuruub, غروب). You should not enter, for instance, the ‘altitude’ of the city you live in, because your local horizon is probably at the same ‘altitude’ as you are.

Unless you know otherwise I recommend that you leave the altitude setting of your prayer time applet to zero.

While on the topic, always check that the times produced by any program that you use correlate closely to the times issued by your local masjid. And if you can then of course looking out the window and seeing the sun set is the best way of knowing when it’s maghrib ;-).