@lawless –
This error condition with MCIP is intentional. The point here is that several of the key meteorological fields from WRF are not defined at WRF’s initialization time (such as cloud coverage, PBL height, among many others), and there is no way to infer this information correctly or at the appropriate horizontal scale from the initial conditions.
You can overcome this issue by starting MCIP at some point after WRF has run. Given your example, you may consider running MCIP starting at 00 UTC 2 January 2012. If you have a need to start CMAQ (and thus, MCIP) at 12 UTC 1 January 2012, then you would need to start WRF at a time prior to that and allow for sufficient spin-up of the meteorological fields in WRF.
–Tanya