Well, the voltage your iPhone receives can vary by the device you use to power it. So if I'm right in saying that the iPhone gauges wether the battery is full or not depending on the amount of time it spends connected to the supply. Your iHome could supplying less voltage to your iPhone than say the standard usb connector.
So it could mess with the figures and the battery life. ( technical language again, apologies ) The iPhone could be displaying a full charge where the battery is only half full.
A good test, make sure you have the battery percentage option turned on in the settings of the iPhone. Do a full charge from your iHome.
Restart the iPhone and see what percentage shows up.