I'm sorry to hear about the difficulties you are experiencing with your custom template. Although I am uncertain which custom template you are referring to, we did update the editor that is used on the custom template creation/revision page earlier this year and it is possible the behavior you mentioned is related to that change.
Assuming the original template which used this image rollover function was created prior to when we updated the editor, the difference you are seeing when you copy the custom template could potentially be a result of the new editor treating that code differently for some reason.
I see that you filed a support case about this and were advised to contact the Developer of the custom template for further assistance with this and, while that may still end up being the best course of action based on the circumstances, I am interested in looking into this further.
I will send you a message through the support case you opened on this subject shortly to request some additional information and we can proceed from there.