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OpenMRS modules and settings disappear and reappear on reboot

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A default Windows install of OpenMRS places its modules and properties files in "%APPDATA%\OpenMRS\". Where "APPDATA" is the home directory Application Data folder of the user that is running Tomcat.

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These problems stem from Windows services being run under the Local System account of the machine on which they are installed. Configure the Apache Tomcat service to start under a specific user account rather than the default "Local System Account". This can be configured in the Services window in Control Panel, Administrative Tools. You should use the same user account when running the installer. 

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<H2><A name="TroubleshootingOpenMRS-OpenMRSwillnotstartanymore.Therearenonmodulefilesinthemodulesdirectory;derby.logand/orvelocity.log"></A>OpenMRS will not start anymore.  There are non-module files in the modules directory; derby.log and/or velocity.log</H2>
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<P>The BIRT Runtime creates various log files in the modules  directory when the BIRT Module is stopped.  OpenMRS won't start if there  are non-modules in the modules directory.  You may find a message in  the event log similar to org.openmrs.module.ModuleException: Module file does not have the correct .omod file extension Module: derby.log</P>
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<P>org.openmrs.module.ModuleException: Module file does not have the correct .omod file extension Module: velocity.log</P>
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<P><B>Solution</B></P>
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<P>Delete the files in the modules directory which aren't modules with an .omod extension. To prevent the derby.log from being created, delete the "org.apache.derby.core_10.1.2.1" directory, under the <PATH birt to>/birt-runtime-2_2_0/ReportEngine/plugins/ directory.</PATH></P>
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Some module pages throw java.lang.ClassNotFoundException

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