Shadow Copies missing / deleted

This may be your issue
 
A Volume Shadow Copy Service (VSS) update package is available for Windows Server 2003

Found this too
Volume Shadow Copy Service snapshots may be unexpectedly deleted after you restart a Windows Server 2003-based computer

I didn't do a defrag or a reboot.

The first link covers more than just a defrag.

There is also this one
Time-out errors occur in Volume Shadow Copy service writers, and shadow copies are lost during backup and during times when there are high levels of input/output

they all show a stable state with no errors

Writer name: 'System Writer'
   Writer Id: {e8132975-6f93-4464-a53e-1050253ae220}
   Writer Instance Id: {d0f140bc-7e10-4757-9c58-e50cece571fc}
   State: [1] Stable
   Last error: No error

Writer name: 'FSRM Writer'
   Writer Id: {12ce4370-5bb7-4c58-a76a-e5d5097e3674}
   Writer Instance Id: {8c5681ee-dce0-4a62-8640-fb1666c1e7e8}
   State: [1] Stable
   Last error: No error

Writer name: 'SqlServerWriter'
   Writer Id: {a65faa63-5ea8-4ebc-9dbd-a0c4db26912a}
   Writer Instance Id: {f18afaf6-cc17-44e7-9173-51d89cfbef83}
   State: [1] Stable
   Last error: No error

Writer name: 'FRS Writer'
   Writer Id: {d76f5a28-3092-4589-ba48-2958fb88ce29}
   Writer Instance Id: {791828b6-3139-4429-8b8f-0d38eb05266f}
   State: [1] Stable
   Last error: No error

Writer name: 'MSDEWriter'
   Writer Id: {f8544ac1-0611-4fa5-b04b-f7ee00b03277}
   Writer Instance Id: {5d918d47-332f-4d09-a24f-28fc8c8b4052}
   State: [1] Stable
   Last error: No error

Writer name: 'WINS Jet Writer'
   Writer Id: {f08c1483-8407-4a26-8c26-6c267a629741}
   Writer Instance Id: {f7d506fe-e5e5-4c6c-9b33-97f5ff4f6007}
   State: [1] Stable
   Last error: No error

Writer name: 'Dhcp Jet Writer'
   Writer Id: {be9ac81e-3619-421f-920f-4c6fea9e93ad}
   Writer Instance Id: {e93fda58-5d8c-4c12-abd0-b6881d609933}
   State: [1] Stable
   Last error: No error

Writer name: 'Certificate Authority'
   Writer Id: {6f5b15b5-da24-4d88-b737-63063e3a1f86}
   Writer Instance Id: {5c3024cf-bc20-4265-8c39-399e20d5e81b}
   State: [1] Stable
   Last error: No error

Writer name: 'WMI Writer'
   Writer Id: {a6ad56c2-b509-4e6c-bb19-49d8f43532f0}
   Writer Instance Id: {384d442a-c679-4fd6-8c2f-e36a34c4c74d}
   State: [1] Stable
   Last error: No error

Writer name: 'Event Log Writer'
   Writer Id: {eee8c692-67ed-4250-8d86-390603070d00}
   Writer Instance Id: {a5a5f846-9895-4e40-80f4-fb77d59639dd}
   State: [1] Stable
   Last error: No error

Writer name: 'IIS Metabase Writer'
   Writer Id: {59b1f0cf-90ef-465f-9609-6ca8b2938366}
   Writer Instance Id: {f82cdd21-1280-47ad-bbc5-dd645328a156}
   State: [1] Stable
   Last error: No error

Writer name: 'BITS Writer'
   Writer Id: {4969d978-be47-48b0-b100-f328f07ac1e0}
   Writer Instance Id: {c3025646-eacb-4b62-a616-c30a6eaee1b2}
   State: [1] Stable
   Last error: No error

Writer name: 'COM+ REGDB Writer'
   Writer Id: {542da469-d3e1-473c-9f4f-7847f01fc64f}
   Writer Instance Id: {9200cd2e-8abc-4e9d-acea-0668450d6ceb}
   State: [1] Stable
   Last error: No error

Writer name: 'NTDS'
   Writer Id: {b2014c9e-8711-4c5c-a5a9-3cf384484757}
   Writer Instance Id: {ba39b403-11b4-413e-a178-a0e201963a2e}
   State: [1] Stable
   Last error: No error

Writer name: 'Registry Writer'
   Writer Id: {afbab4a2-367d-4d15-a586-71dbb18f8485}
   Writer Instance Id: {d7509dda-6da9-4dd7-846d-1f305719afef}
   State: [1] Stable
   Last error: No error

I get the following Information event when my backup kicks in at around 6pm but it doesn't show up as an error.  Also it shows up every day so I don't think that's what causing it.

Event Type:      Information
Event Source:      ESENT
Event Category:      ShadowCopy
Event ID:      2003
Date:            24/04/2009
Time:            6:01:15 PM
User:            N/A
Computer:      RPS3
Description:
lsass (452) Shadow copy 48 freeze stopped.

oh oh

but there was over 200GB of free space

Event Type:      Error
Event Source:      VolSnap
Event Category:      None
Event ID:      35
Date:            24/04/2009
Time:            1:39:50 PM
User:            N/A
Computer:      RPS3
Description:
The shadow copies of volume E: were aborted because the shadow copy storage failed to grow.


Event Type:      Warning
Event Source:      VolSnap
Event Category:      None
Event ID:      24
Date:            24/04/2009
Time:            1:02:39 PM
User:            N/A
Computer:      RPS3
Description:
There was insufficient disk space on volume E: to grow the shadow copy storage for shadow copies of E:.  As a result of this failure all shadow copies of volume E: are at risk of being deleted.



and I have about 60 of these ones

Event Type:      Information
Event Source:      VolSnap
Event Category:      None
Event ID:      33
Date:            24/04/2009
Time:            1:02:38 PM
User:            N/A
Computer:      RPS3
Description:
The oldest shadow copy of volume E: was deleted to keep disk space usage for shadow copies of volume E: below the user defined limit.

That event ID led to here
http://support.microsoft.com/kb/830575/en-us 

Looks like you found the culprit

I'm wondering how come it thought there was no free space.  There was 200GB free.