I just installed a new USB tuner as a backup. But perhaps due to diff design/chipset, the tuner is picking up a slightly different channel lineup. It is missing a channel that I watch occationally. So there is a potential which the tuner is picked to record the channel it does not receive while I am away.

Is there a way to assign the channels to different numbers? E.g. Instead of 1021, make it 2021. So I know which tuner that I am recording? How does HDHomeRun solve this problem?

If both tuners are the same type: Analog or Digital, then you cannot specify certain stations on each tuner.  The tuners are considered exactly the same and must be configured the same. 

So if both tuners are NTSC (Analog over the air or cable TV) then both tuners use the same guide.  If 1 tuner is using a STB, then both tuners need STBs.

I recommend figuring out why the new card is not receiving a channel that it should get. 

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1: Dimension 9200 - Vista Ult, 2.4GHz Q6600 Core2Quad, 4GB RAM, 160GB, 750GB, 500GB USB, Nvidia 8300GS, PVR-150, HDTV Wonder, Vbox 3560, X360, DMA2100

2: HP m376n - MCE 2005, 2.6 P4 w/HT, 1GB RAM, 250GB, 400GB USB HD, Nvidia 6200, Emuzed MAUI, X360