Every time that a thinner cloud layer is reported to be lower than a more thick layer, it seems like the thicker higher layer is surpressed. I have ASE B655 for FS9.For example, now I made a short flight around ESSA and metar reported FEW006 and BKN020 and I don't think I experienced any broken thicker layer at 2000ft. Also in FS if you select 'Weather' from the 'World' drop down menu, while flying, it only says 'Light coluds'.Is this correct? It seems like FS is forgetting the higher broken layer.

FS has a hard time with "conflicting" cloud layers, and it's normal to see one layer suffer due to another one. As we must adhere to METAR accuracy this isn't avoidable unfortunately. But you may seeing the effects of interpolation more than anything else, and must consider other stations in the vicinity effecting things at your location. For a good comparison you have to be directly over the station reporting the data you are looking at.The FS9 Wx dialog, for comparison of a station's data in the sim vs. Active Sky, must be used via the "single station" method. By default it will show irrelevant global conditions which are not used in FS9/Active Sky. But the station-based cloud layers should indeed match.