Bukkit

Describe to us the issue that you're having:
In the versions of bukkit: (1.4.5-R1.0, 1.4.6-R0.1) bpermissions made a lot of errors (see first error log below), and after updating bpermissions (to 2.9.25c) the errors were gone but permissions were not working at all making other plugins error (see second error log below), when downgrading to bukkit 1.4.5R0.2 there are no errors and all permissions work correctly,

as other people have also seen, I have found  a null player listed in the players list in the world files in the bpermissions plugin folders,
yet there is no player named 'null' in the player files (normal inventory files).
  'null':
    permissions: []
    groups:
    - default

Which steps will reproduce this problem?:
1) using bukkit 1.4.5-R0.2-Beta with various plugins,
2) update bukkit to 1.4.6 R0.1 or 1.4.5 R1.0
3) the permissions may not work correctly,
....

Do you have an error log of what happened?
### Error log from before bpermissions update: ###
2012-12-20 23:45:47 [WARNING] [bPermissions] Task #5 for bPermissions v2.9.24 generated an exception
java.lang.NoClassDefFoundError: Could not initialize class de.bananaco.bpermissions.imp.BukkitCompat
    at de.bananaco.bpermissions.imp.SuperPermissionHandler$SuperPermissionReloader.run(SuperPermissionHandler.java:58)
    at org.bukkit.craftbukkit.v1_4_6.scheduler.CraftTask.run(CraftTask.java:53)
    at org.bukkit.craftbukkit.v1_4_6.scheduler.CraftScheduler.mainThreadHeartbeat(CraftScheduler.java:345)
    at net.minecraft.server.v1_4_6.MinecraftServer.r(MinecraftServer.java:530)
    at net.minecraft.server.v1_4_6.DedicatedServer.r(DedicatedServer.java:224)
    at net.minecraft.server.v1_4_6.MinecraftServer.q(MinecraftServer.java:494)
    at net.minecraft.server.v1_4_6.MinecraftServer.run(MinecraftServer.java:427)
    at net.minecraft.server.v1_4_6.ThreadServerApplication.run(SourceFile:849)

## error log after bpermissions update ##
## this is what hawkeye and worldguard show, the only plugins complaining, but all plugins were not working as if they had no permissions configured, multiverse core / portals was not allowing users to other worlds even though it was correctly configured ##
2012-12-21 04:32:09 [SEVERE] Could not pass event EntityChangeBlockEvent to HawkEye v1.0.7b
org.bukkit.event.EventException
2012-12-21 04:32:11 [SEVERE] Could not pass event EntityChangeBlockEvent to WorldGuard v674-6d09b18
org.bukkit.event.EventException

Which version of bPermissions are you using?: (Please don't say "latest"!!!)
before, 2,9,24 or 25
After update 1.9.25c

Which version of CraftBukkit?: (Please don't say "latest"!!!)
Works stably on Bukkit Beta build 1.4.5 r0.2
does not work on any 1,4,6 bukkit or bukkit 1.4.5 recommended R1.0

Which OS?
linux

Any other information we may need (plugins, configs, etc):
All plugins which require permissions initially had problems,
After update and using bukkit 1.4.6, Hawkeye and Worldguard will error, as in the error log above

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Same.