In reality you are dealing with two different monsters:
the SCS method was developed based on only a few watersheds and the results of the method are based on the predefined rainfall distribution (i.e. Type II, III, etc.), the standard or modified unit hydrograph you are using, CN, and the time of concentration. Also, you must understand that if you input a 100-yr rainfall amount it will be based on a statistical anlyses of precipitation data.
The USGS method is based on a regression of years of record of streamflow data which are not tied to a particular rainfall event. The reccurence interval of certain flow events allows the determination of the peak flow for a 100-yr event. Meaning that the actual rainfall hydrographs and distributions are completely different than SCS.
Thus, it is highly unlikely that the flows for a SCS analyses and USGS equations will ever match. The solution to your problem though is to look at both and the data behind it to determine which best fits your situation. A lot of times it is accepted in practice to adjust the time of concentration in the SCS method (since it is the value with the greatest uncertainity in the SCS method) such that the peak flow approximately matches that from the USGS method. However, this is based on your engineering judgement.