It is very unlikely the act of copying the clips caused any issues.
Check the framerate in the interpret footage of the clips in the project window to see to what framerate it is set for. Correct this if neccessary.
IIRC, the Nikon D-90 encodes to MJPEG. Which MJPEG CODEC do you have? Both the MainConcept and the Morgan get high marks. Others, not so much.
Are you in PAL-land, hence the 25 fps? What is the exact description of the camera's 24 fps setting? Is it some form of 24p, or 24pA? You'll probably have to delve into the manual for this, as full descriptions will not likely be on Nikon's site, and though popular, not many in this forum use a D-90 for capturing motion.
As a bit of a followup, you might be best off creating a Sequence with a custom setting for your frame size and 24p as the frame rate.
Jim has also written several articles on 24p/24pA material. Some were before the forum changeover, but I think someone found them and there are now current links to many of those, plus the discussions that accompanied them. There might be some suggestions in those, that would apply to your footage, and help you with the Project/Sequence settings.
Thank you for the ideas. I am not sure what codec I have but I will look it up.
With the D90, I was shooting in HDV- so my frame rate is 24p not 24pA.
I have tried creating a custom sequence for my footage. I am using the HDV720p editing mode, because it seems to be the only editing mode that is HDV and is 1280x720 (which is the size of my footage). However, there is no option to edit with 24p with this setting, only with 23.976 fps. Could this be causing my problem?