I realize this is an old thread, but just in case the following would help someone in the future:
I've been using 64gb SDXC1 cards in my D5000 for quite awhile and thought I had no problems. Recently I tried to use interval timer shooting but was unable. Spent quite a bit of time searching for reasons & ran across many hypotheses, almost none of which helped.
However, someone suggested they'd solved their problem by switching to a smaller capacity card. Seeing one of the comments above about the D5000 not being compatible with SDXC cards, I decided to try an SDHC card in place of the SDXC card. It worked and interval timer shooting functionality returned.
Unfortunately I don't have many SDHC cards lying around, so I can't determine what maximum size SDHC card will work and provide functioning interval timer shooting.
I never thought the suitability of a particular card would be partial. I assume they would work or not. If they worked at all, I assumed everything would work. Apparently that's a poor assumption.
Howard
edited to correct sloppy acronyms