[mandytan]

Using a GC-FID (Gas Chromatography-Flame Ionization Detector) and a capillary column, an experiment was carried out. It was noticed that all the peak areas of the sample & blank(ethanol) were decreased significantly when compared with a previous analysis. (i.e. previous peak area~200 versus current peak area~ 50).Could it be that the decreased peak areas are due to the column not being installed correctly?
Although all the peak areas were decreased, by area normalisation, we could still obtain satisfactory results for our sample. 
In your opinion, are these results considered acceptable?

[Jasim]

If the column weren't installed correctly, you'd most likely have other issues than decreased peak area - if you got any peaks at all.

Did you verify that all parameters are the same and nothing has been changed? Are you sure the peak areas have actually decreased and it isn't a calculation issue with whatever software is doing your data processing?