What method are you using now?
Star Trek has what is called structural protection, this means that if it isn't correctly ripped you get the scenes in the wrong order. AnyDVD, the later versions, ie 6.5.9.5 posted earlier, can fix this up and you should be able to back up OK.
Transformers 2 has similar protection and is also handled OK by AnyDVD 6.5.9.5.
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