This is a MCE limitation. Dual tuner usage in Media Center Edition 2005 requires both TV provider sources (channel lineups) to be identical. For example, you can configure two set-top boxes or two cable out of the wall connections, but you cannot use one set-top box and one out of the wall cable connection or one satellite and one antenna connection. The reason for this is pretty simple. Windows XP Media Center 2005 uses a single Program Guide and uses the "first available analog tuner" to complete each task that requires an analog TV tuner.
If you have two different set-top box models from the same provider, you can use them as long as they both receive the same programs on the same channels. For example, you can use a Motorola/General Instruments DCT5100 and a DCT6200 set-top box to configure dual tuner support.