Following is an example I am suffering from now, just don't know how it could happen and the solution for us so far is just to manually move impacted columns back to the right position, which is stupid of course:
1. Columns (Latitude and Longitude) are at the begining of the excel file:
2. After imported into the FME, the order of these two columns (Latitude and Longitude) changed and moved to the last for no reason: