We also see high CH4 and N2O in our retrievals and also suspect that insufficient altitude resolution of T could cause this trouble. More realistic N2O and CH4 values were retrieved from MIPAS S2 mode measurements (which hints in the same direction, because also T is better resolved there). Some further tests on this are planned (starting next week). I will keep you posted.
I think it is now clear that the operational processor is not flagging all clouds and removing them from the retrieval. The problem with the processor has not yet been identified but an IFAC retrieval shows that the prototype processor and auxiliary data file work fine. In particular we have seen that many of the PSCs are not removed in the Antarctic spring leading to anomalous zonal means for gases. Also, some tropical clouds are missed which can also lead to high values of CH4 etc. in the mean values at altitudes below 20 km.