Tell us the procedures you are using now to copy your dvd's and we will probably be better able to help you.
There are many different ways to copy a dvd. One way is to use a program like DVDDecrypter or DVDShrink to get the movie onto the hard drive, then get it to the correct size with Shrink or NeroRecode, or even an encoder program like DVDRebuilder.
Then burn their output with Nero using the DVDVideo mode. This should be all that is necessary.
If you don't have Nero, you can use two free programs to decrypt, resize and burn. DVDDecrypter in combination with DVDShrink can do this using Decrypter's ability to burn image files. Look through some of the tutorials here at cdfreaks for these programs. There are other tutorials available online also, such as the ones at doom9 or mrbass.org