[OSX] FTB Ultimate Server cannot see mods folder

[AtomicCuttlefish]

My friend and I are trying to run a FTB Ultimate server, and while the server itself seems to start up fine, when either of us tries to connect, the following occurs:

    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod OmniTools was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod ChargePads was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod WR-CBE|Core was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod ObsidiPlates was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod WR-CBE|RedPower was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod Forestry was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod EnderStorage was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod BinnieCore was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod mmmPowersuits was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod BuildCraft|Energy was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod ChickenChunks was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod AppliedEnergistics was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod BuildCraft|Silicon was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod BuildCraft|Core was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod SecretRoomsMod was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod ExtraBees was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod Mystcraft was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod WR-CBE|Addons was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod BuildCraft|Factory was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:35 [WARNING] [ForgeModLoader] The mod BuildCraft|Builders was not found on the server you connected to, but requested that the server side be present
    2013-03-09 18:29:36 [SEVERE] [fml.ItemTracker] FML has detected item discrepancies
    2013-03-09 18:29:36 [SEVERE] [fml.ItemTracker] Missing items : {}
    2013-03-09 18:29:36 [SEVERE] [fml.ItemTracker] Mismatched items : {343=(Item 343, Type uv, owned by Minecraft, ordinal 2, name null, claimedModId null, Item 343, Type railcraft.common.carts.ItemCartVanilla, owned by Railcraft, ordinal 2, name rc.item.cart.furnace, claimedModId null), 102=(Item 102, Type amp, owned by Minecraft, ordinal 1, name null, claimedModId null, Item 102, Type powercrystals.minefactoryreloaded.decorative.BlockVanillaGlassPane, owned by MFReloaded, ordinal 0, name blockVanillaGlassPane, claimedModId null), 342=(Item 342, Type uv, owned by Minecraft, ordinal 1, name null, claimedModId null, Item 342, Type railcraft.common.carts.ItemCartVanilla, owned by Railcraft, ordinal 1, name rc.item.cart.chest, claimedModId null), 79=(Item 79, Type akr, owned by Minecraft, ordinal 0, name null, claimedModId null, Item 79, Type powercrystals.minefactoryreloaded.decorative.ItemBlockVanillaIce, owned by MFReloaded, ordinal 0, name blockVanillaIce, claimedModId null), 328=(Item 328, Type uv, owned by Minecraft, ordinal 0, name null, claimedModId null, Item 328, Type railcraft.common.carts.ItemCartVanilla, owned by Railcraft, ordinal 0, name rc.item.cart.basic, claimedModId null)}

This only occurs on OSX, on windows the server can work fine, though we cannot run it on windows due to memory limitations.

EDIT: As far as we can tell, everything has the permissions set correctly.

EDIT2: Interestingly enough, removing xycraft and using the following ServerStart.command worked:

#!/bin/bash
cd "$( dirname "$0" )"
java -Xms2028M -Xmx4048M -jar SERVERFILENAME.jar -o true