Its possible some of the files arent satisfying rsync's default size & date. Get rsync to transfer based on check sums instead. It will be slower, but if the file has changed in anyway, it will be transfered.
rsync -cav <source> <destination>
If you want to check that it will transfer the files you want, add -n to the end of the command to get a dry run. You can then check the list for missing files, or even easier, if you have a specific filename that you know wasn't being transferred before, just grep for it!
rsync -cav <source> <destination> -n | grep some-missing-filename
UPDATE: If you're not sure if the contents of the folders are the same, then you can check easily with the following:
on each server:
cd /to/root/of/your/website
find . | md5sum
And then compare the md5 check sum which is output, if the number is the same, then you have the same files (e.g. file1 on server1 and on server2) although this doesn't account for the file contents being different
If you want to see what files exist in one, but not in another, then you can of course output directory listings to files:
cd /to/root/of/your/website
find . > server1.txt
... on both servers, and then
diff server1.txt server2.txt
Just one final thought:
scp -r user@server1:/path/to/website /path/to/website