Strange behaviour 10.7.1 Lion Server

My Macbook Pro (5,1) has been setup as a Lion Server (I have the issue of keepoing the thing awake but can live with that).
Two issues I am experiencing which I can not work out:
1) Wake on LAN (WOL) will not work via the Internet. I have a Time Capsule as my router and the Mac is hardwired over gigabit ethernet. It works fine on my LAN but will not wake the MBP over the WAN?
2) The local desktop keeps freezing when left running for any period of time. I am not sure if it is Lion or my setup.
The MBP is "docked" in a Henge dock it has all connections utilised (FW/USB etc).
I have an external display Dell U2410 connected via Mini Display Port  and I am using the Magic Mouse (on Bluetooth) and allow this device to wake on Bluetooth is also enabled.
The Firewire is connected to a WD My Book Studio Edition II for Time Machine backups (as the Time Capsule is used by my MacBook Air for Time Machine Backups)
When I have finished on the machine I always log off the active user and power off the monitor.
I leave the machine running until it sleeps (where I can WOL if I need it while still working on LAN).
When I return after a period of time the local desktop (menu bar, dock etc) are totally unresponsive, I cannot do anything at all locally on the machine.
However if I log in via my MacBook Air using screen sharing I can drive the desktop totally normally?
I usually have to reboot the MacBook Pro in order to get the local desktop to be responsive again?
Has anyone else seen this or have any idea what may be causing these issues?
Many thanks in advance.......

I have solved 1) and I can now WOL over WAN but I am still experiencing issues with 2).
Has no-one else experienced issues with the local desktop becomning unresponsive?
If I leave the MBP up and running for any extended period of time I repeatably have this issue and it is driving me nuts.
I can find no particular thing that triggers this from what I can see.
The only way to resolve is to log in remotely via screen sharing and restart it!
Anyone? Please.......

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    Hi all,
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    Thanks in advance.

    Hi Paul,
    Honestly, I'm still trying to figure out all broken things reported by tests :( Guess Jesper's suggestion about adding a new 2008 DC to get rid of 2003 and start checking again after that may be best option.
    I'll try to summarize list of things I believe are wrong:
    running
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    may be for a bug old sys admin had when clonning from his 2008R2 template, that forgot to change SID... I already noticed 1 year ago our print server shared SID with those DC, guess there may be more servers sharing SID too :-(
    Within Starting test: Replications, I see few messages at Replication Latency Check, such as the one for CN=Schema, CN=Configuration, DC=<ourdomain>: 
    Latency information for 35 entries in the vector were ignored.
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    On Services test, I see an 
       Invalid service type: RpcSs on DC-DOMAIN-3, current value
                WIN32_OWN_PROCESS, expected value WIN32_SHARE_PROCESS
    On SystemLog, I see LOTS of warnings/errors such as:
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                Time Generated: 07/28/2014   08:21:54
                (Event String (event log = System) could not be retrieved, error
                0x503)
             An error event occurred.  EventID: 0xC0000003
                Time Generated: 07/28/2014   08:22:18
                (Event String (event log = System) could not be retrieved, error
                0x3afc)
    Missing entries on DNS (we've a static DNS)
    netdiag.exe /v > c:\netdiag.log Showed again DNS problems such as our primary DNS pointing to all DC, secondary
    DNS pointing just to DC with FSMO roles,...
    repadmin.exe /showrepl * /verbose /all /intersite > c:\repl.txt  Gave no errors, now I must check in detail
    if every replica is correct
    And finally,
    dnslint /ad /s "ip address of your dc"  gave more DNS problems:
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    One or more DNS servers did not respond to UDP queries
    One or more zone files may have expired
    SOA record data was unavailable and/or missing on one or more DNS servers
    Sumarizing, guess it will be better to fix DNS problems, promote new 2008R2 DC to get rid of 2003 one, promote domain to 2008 too, check again for messages and relationship with other domain, and then come back here for support if needed 
    EDIT: Almost forgot to talk about SYSVOL folder. As said before, there are 426 GPO folders inside Policies. Of them, 375 have an inetres.adm files in it (smallest one 1398 KB, almost all of them 2307 or 2707 kb).... 

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