If it's the downloaded tracks that have no silence at the end, then that is the fault of whoever released them in that form. I have found (so far) that purchased tracks all do have a few seconds of silence at the end.
If it is only one album in your case, then there is a work round though it is a bit laborious. Make yourself a track of 3 seconds silence (e.g. find a track with some silence at the end, set the Start Time in Get Info to 3 seconds from the end and leave the Stop Time blank; 'Convert Selection...' to a low bitrate format; rename it "3 seconds silence").
Then for each track in your album, use the free download 'Join Together' (
http://dougscripts.com/itunes) to join the silence track to the end of it, and repeat until you have it joined to each track.
If anyone knows a better or quicker way, that would be useful too! (I searched Doug Scripts for an "add silence" script, but there doesn't seem to be one. You could always try contacting Doug and ask him if this is possible to do?)