I have fisheye running on windows server 2008, and it was working fine. I came in today, and the service won't stay running. Here is the output from the wrapper.log:
STATUS | wrapper | 2013/06/21 12:03:31 | --> Wrapper Started as Service
STATUS | wrapper | 2013/06/21 12:03:32 | Launching a JVM...
INFO | jvm 1 | 2013/06/21 12:03:32 | java version "1.7.0_25"
INFO | jvm 1 | 2013/06/21 12:03:32 | Java(TM) SE Runtime Environment (build 1.7.0_25-b16)
INFO | jvm 1 | 2013/06/21 12:03:32 | Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)
INFO | jvm 1 | 2013/06/21 12:03:32 |
INFO | jvm 1 | 2013/06/21 12:03:32 | JDK 1.5 detected, registering Java Service Wrapper MBean
INFO | jvm 1 | 2013/06/21 12:03:32 |
INFO | jvm 1 | 2013/06/21 12:03:32 | WARNING - Unable to load the Wrapper's native library 'wrapper.dll'.
INFO | jvm 1 | 2013/06/21 12:03:32 | The file is located on the path at the following location but
INFO | jvm 1 | 2013/06/21 12:03:32 | could not be loaded:
INFO | jvm 1 | 2013/06/21 12:03:32 | 
\Atlassian\fisheye\wrapper\lib\wrapper.dll
INFO | jvm 1 | 2013/06/21 12:03:32 | Please verify that the file is readable by the current user
INFO | jvm 1 | 2013/06/21 12:03:32 | and that the file has not been corrupted in any way.
INFO | jvm 1 | 2013/06/21 12:03:32 | System signals will not be handled correctly.
INFO | jvm 1 | 2013/06/21 12:03:32 |
INFO | jvm 1 | 2013/06/21 12:03:32 | Wrapper (Version 3.1.2) http://wrapper.tanukisoftware.org
INFO | jvm 1 | 2013/06/21 12:03:32 |
INFO | jvm 1 | 2013/06/21 12:03:32 | WARN: your default encoding (windows-1252) does not support unicode.
INFO | jvm 1 | 2013/06/21 12:03:32 | This is likely to cause problems if any of the filenames, branch names or tag names in one of your repositories contain unicode characters.
INFO | jvm 1 | 2013/06/21 12:03:32 | Update your locale settings or start with the -Dfile.encoding=UTF-8 option to avoid these problems.
INFO | jvm 1 | 2013/06/21 12:03:33 | 2013-06-21 12:03:32,990 INFO - Using log4j configuration file: \Atlassian\fisheye\log4j.xml
INFO | jvm 1 | 2013/06/21 12:03:33 | 2013-06-21 12:03:33,005 INFO - FishEye arguments: []
INFO | jvm 1 | 2013/06/21 12:03:33 | 2013-06-21 12:03:33,005 INFO - FishEye/Crucible 2.10.3 (20130318234358), Built on 2013-03-19
INFO | jvm 1 | 2013/06/21 12:03:33 | 2013-06-21 12:03:33,005 INFO - Logging started (Oracle Corporation|23.25-b01|C:\Java\jdk1.7.0_25\jre|Windows Server 2008 R2|amd64|6.1|maxmem=910MB)
INFO | jvm 1 | 2013/06/21 12:03:35 | 2013-06-21 12:03:35,158 INFO - UpgradeManager started.
INFO | jvm 1 | 2013/06/21 12:03:35 | 2013-06-21 12:03:35,205 INFO - loading config from file: \Atlassian\fisheye\config.xml
INFO | jvm 1 | 2013/06/21 12:03:35 | 2013-06-21 12:03:35,595 INFO - FishEye: Evaluation License registered to Mainstream Technologies.
INFO | jvm 1 | 2013/06/21 12:03:35 | 2013-06-21 12:03:35,611 INFO - Your license expires in 14 days
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,375 INFO - System property fisheye.p4.disable.ancestry using value: false (default is false)
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,375 INFO - System property fisheye.p4.disable.branchspecs using value: false (default is false)
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,391 INFO - System property fisheye.disable.suffixpaths using value: false (default is false)
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,391 INFO - System property fisheye.svn.index.trunk.content.only using value: false (default is false)
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,391 INFO - System property fisheye.jira.activity.enable using value: false (default is false)
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,391 INFO - System property fisheye.jetty.jmx.enable using value: false (default is false)
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,422 INFO - Adding secondary content dir of \Atlassian\fisheye\content
INFO | jvm 1 | 2013/06/21 12:03:36 | 2013-06-21 12:03:36,453 INFO - Server started on solomonsvn.mainstream-tech.com:8060 (http) (control port on 127.0.0.1:8059)
INFO | jvm 1 | 2013/06/21 12:03:37 | WARN: your default encoding (windows-1252) does not support unicode.
INFO | jvm 1 | 2013/06/21 12:03:37 | This is likely to cause problems if any of the filenames, branch names or tag names in one of your repositories contain unicode characters.
INFO | jvm 1 | 2013/06/21 12:03:37 | Update your locale settings or start with the -Dfile.encoding=UTF-8 option to avoid these problems.
INFO | jvm 1 | 2013/06/21 12:03:37 | INFO - Using log4j configuration file: \Atlassian\fisheye\log4j-client.xml
INFO | jvm 1 | 2013/06/21 12:03:37 | INFO - FishEye arguments: []
INFO | jvm 1 | 2013/06/21 12:03:38 | 2013-06-21 12:03:38,075 ERROR - Failed to remove shutdown hook
INFO | jvm 1 | 2013/06/21 12:03:38 | java.lang.IllegalStateException: Shutdown in progress
INFO | jvm 1 | 2013/06/21 12:03:38 |at java.lang.ApplicationShutdownHooks.remove(ApplicationShutdownHooks.java:82)
INFO | jvm 1 | 2013/06/21 12:03:38 |at java.lang.Runtime.removeShutdownHook(Runtime.java:239)
INFO | jvm 1 | 2013/06/21 12:03:38 |at com.cenqua.fisheye.ctl.ShutdownService.stopImpl(ShutdownService.java:270)
INFO | jvm 1 | 2013/06/21 12:03:38 |at com.cenqua.fisheye.ctl.ShutdownService.handleStop(ShutdownService.java:256)
INFO | jvm 1 | 2013/06/21 12:03:38 |at com.cenqua.fisheye.ctl.ShutdownService.handleClient(ShutdownService.java:123)
INFO | jvm 1 | 2013/06/21 12:03:38 |at com.cenqua.fisheye.ctl.ShutdownService.access$200(ShutdownService.java:37)
INFO | jvm 1 | 2013/06/21 12:03:38 |at com.cenqua.fisheye.ctl.ShutdownService$3.run(ShutdownService.java:87)
INFO | jvm 1 | 2013/06/21 12:03:38 |at java.lang.Thread.run(Thread.java:724)
INFO | jvm 1 | 2013/06/21 12:03:38 | FishEye Shutdown successfully
ERROR | wrapper | 2013/06/21 12:04:10 | Shutdown failed: Timed out waiting for signal from JVM.
ERROR | wrapper | 2013/06/21 12:04:10 | JVM did not exit on request, terminated
STATUS | wrapper | 2013/06/21 12:04:11 | <-- Wrapper Stopped
