The log you posted, disagrees with the output you posted from "SELECT @@version":
Microsoft SQL Server 2005 - 9.00.5069.00 (Intel X86) Aug 22 2012 16:01:52 Copyright (c) 1988-2005 Microsoft Corporation Standard Edition on Windows NT 5.2 (Build 3790: Service Pack 2)
The log file you posted is something else:
2013-07-29 07:59:04.53 Server Microsoft SQL Server 2005 - 9.00.1399.06 (Intel X86)
Oct 14 2005 00:33:37
Copyright (c) 1988-2005 Microsoft Corporation
Express Edition on Windows NT 5.1 (Build 2600: Service Pack 3)
Maybe that's a local Express instance running on your local machine. (And to which you have not applied any service packs!).
I was of course interesting in the errorlog for the SQL Server where you have problem with running the CLR.
If this is happening to any CLR module, maybe your DBA should try restarting SQL Server?
Erland Sommarskog, SQL Server MVP, www.sommarskog.se