Guibo, which is a rubber /cloth coupling between the driveshaft and the transmission... when they start to disintegrate they can make a flapping sound, or if you have a bad center bearing mount on the driveshaft and suddenly reverse the load it can make a scraping flapping noise.. Thats the first place i would look.. The 3rd gear gear change is unrelated... Are you sure thats not just the normal lag when the engine is cold? There is a lag built in when the engine is cold to delay the shift so that the engine runs longer at higher rpms so it will warm up quicker.