-After reading your post, I did the following:
-one player currently has a chunkloader in the nether (buildcraft pump I think). Verified open by using /chunkloaders.
-/chunkloaders does not show any open chunks in Twilight Forest (TF)
-I enter the TF and place the chunkloader:

2013-02-28 11:07:05 [INFO] [ForgeModLoader] Loading dimension 7 (Mote Prime) (ho@57ff78b0)
2013-02-28 11:07:05 [INFO] [STDOUT] Cache loaded.  Size = 31956
2013-02-28 11:07:05 [INFO] [STDOUT] Readded hashes, hash size = 31956
2013-02-28 11:07:05 [INFO] [ForgeModLoader] [Thaumcraft] Loaded 146 aura nodes for world 7
2013-02-28 11:07:06 [INFO] [STDOUT] Sending serverside check to: Haruchai
2013-02-28 11:07:21 [FINE] [ForgeModLoader] Set beekeeping mode for a world to NORMAL

-I exit the TF and verify that a chunk is open (true):

2013-02-28 11:08:29 [INFO] [STDOUT] Sending serverside check to: Haruchai

-I quit and restart the server:

2013-02-28 11:10:30 [INFO] [Minecraft] Haruchai lost connection: disconnect.quitting
2013-02-28 11:10:30 [INFO] [STDOUT] Unloading Player: Haruchai
2013-02-28 11:10:52 [INFO] [Minecraft] [Server] Server is restarting. World is being saved.
2013-02-28 11:10:52 [INFO] [Minecraft] Turned on world auto-saving
2013-02-28 11:10:52 [INFO] [Minecraft] Saving...
2013-02-28 11:10:52 [INFO] [Minecraft] Saved the world
2013-02-28 11:10:52 [INFO] [Minecraft] Stopping the server

-Here's the end of the log after the server restart (with chunkloaders in the Nether and TF):

2013-02-28 11:14:46 [INFO] [STDOUT] Loading NEI
2013-02-28 11:14:49 [WARNING] [Minecraft] Can't keep up! Did the system time change, or is the server overloaded?
2013-02-28 11:14:52 [FINE] [ForgeModLoader] Set beekeeping mode for a world to NORMAL
2013-02-28 11:14:59 [INFO] [Forestry] Created player '[Forestry]' for Forestry.
2013-02-28 11:14:59 [INFO] [Forestry] Opped player '[Forestry]'.
2013-02-28 11:15:10 [INFO] [ForgeModLoader] [Thaumcraft] Removed -903 aura nodes when world 1 unloaded.
2013-02-28 11:15:10 [INFO] [ForgeModLoader] Unloading dimension 1
2013-02-28 11:15:17 [SEVERE] [ForgeModLoader] Detected leaking worlds in memory. There are 2 worlds that appear to be persisting. A mod is likely caching the world incorrectly
2013-02-28 11:15:17 [SEVERE] [ForgeModLoader] The world 1155623c (Mote Prime) has leaked.

-I log on the server:

2013-02-28 11:16:36 [INFO] [STDOUT] Loading Player: Haruchai
2013-02-28 11:16:36 [INFO] [STDOUT] Sending serverside check to: Haruchai
2013-02-28 11:16:36 [INFO] [Minecraft] [Server] Welcome back, Haruchai
2013-02-28 11:16:36 [INFO] [Minecraft] You whisper to Haruchai: Haruchai! Welcome to Mote Prime.
2013-02-28 11:16:37 [INFO] [PortalGun] [1.4.7v3] Recieved client info from Haruchai

-I go through the TF portal:

2013-02-28 11:18:02 [INFO] [STDOUT] Sending serverside check to: Haruchai

-I remove the chunkloader and come back through the portal:

2013-02-28 11:18:22 [INFO] [STDOUT] Sending serverside check to: Haruchai
2013-02-28 11:19:10 [INFO] [ForgeModLoader] [Thaumcraft] Removed -595 aura nodes when world 7 unloaded.
2013-02-28 11:19:10 [INFO] [ForgeModLoader] Unloading dimension 7

-I verify that the chunk is unloaded in the TF (ie, /chunkloaders does not show an open chunk in dimension 7): true
-Despite showing no chunks loaded, the leak persists:

2013-02-28 11:19:17 [SEVERE] [ForgeModLoader] Detected leaking worlds in memory. There are 3 worlds that appear to be persisting. A mod is likely caching the world incorrectly

2013-02-28 11:19:17 [SEVERE] [ForgeModLoader] The world 318ffaf0 (Mote Prime) has leaked.