@turboccc and Kanopus
I opened the 3MB logo and edited file by loading the tmp.png auto generated by gir editor as the new logo. Saved the result and the new file size is only 11KB. Sound like the 'truncating' has been carried out by Gir Editor.
At least now I am not concerned at the large discrepancy in logo file sizes. Clearly some logo files had been truncated and some not.