It sounds to me that you are using FS2002 aircraft for FS2004.  In most cases this will not work and the result be what you are seeing a plane with no landing gear and sometimes the jet engines will not show any fans in them they will appear to be hollow. The aircraft used in FS2004 were either built with GMAX or some other program that I can not rember its name. I have heard that you can fix the gear problem sometimes, if you check some of the posts by ROLLERBALL I think he had one answer to the gear problem.
But even that did not always help, my advise would be to can it and replace with a FS2004 version.  8)

Just to clarify. The later FS2002 aircraft created with Gmax or FS Design Studio Version 2 (FSDS2) should work perfectly well in FS2004. It's only the older designs created with FSDS1 that aren't fully compatible. The gear animation on these aircraft is usually OK, providing you click the No option on the "Incompatible 3rd Party Software" warning message on first selecting the aircraft in FS9. You can do the same thing by editing fs9.cfg in Notepad. Look for the problem aircraft listed under the [FrameCallNoWarn] header & change the value from 0 to 1. This should fix the gear animation but does not generally fix animated prop disks or turbines.