One possibility, which is what I suspect happened, is that when you converted from stock to craftbukkit, the nether folder did not get moved properly. When you run craftbukkit for the first time in a folder that is already a stock server, it has to make some changes.
One of those changes is moving the nether and the end region/anvil file folders into their own folders. Your world is now contained in 3 folders. If you stayed with the default name of world then the folders would be named world, world_nether, and world_the_end. Originally, the world folder contained two folders named DIM-1 and DIM1. These folders contained the region/anvil file folders of the nether and the end. When craftbukkit is first run it should create the folder world_nether and move DIM-1 from the world folder to the _nether folder. The same of DIM1 to the _the_end folder. If you had looked in console on first run you may have seen something like this:
[88:88:88 INFO]: ---- Migration of old nether folder required ----
[88:88:88 INFO]: Unfortunately due to the way that Minecraft implemented multiworld support in 1.6, Bukkit requires that you move your nether folder to a new location in order to operate correctly.
[88:88:88 INFO]: We will move this folder for you, but it will mean that you need to move it back should you wish to stop using Bukkit in the future.
[88:88:88 INFO]: Attempting to move world\DIM-1 to world_nether\DIM-1...
[88:88:88 INFO]: Success! To restore nether in the future, simply move world_nether\DIM-1 to world\DIM-1
[88:88:88 INFO]: ---- Migration of old nether folder complete ----
Something similar for the end folder. Perhaps this operation failed. If it did fail, the DIM-1 folder may still be in the world folder.
If it is:
- Stop the server.
- Download a full backup copy of your server files (do this either way and do it regularly)
- Go into the current _nether folder and rename DIM-1 to something else (ex:DIM-1_bak)
- Move the original DIM-1 folder from the world folder to the _nether folder.
- Start the server and see if the original nether is back.