JT-19987: Something has gone wrong with our database

What steps will reproduce the problem?
1. Open YouTrack v3.3
2. Enter a keyword, like "frame", in the search field
3. Click Search

What is the expected result?
List of issues with references to the word frame, such as frame.js

What happens instead?
An "Opps! Something went wrong" error message.

===Environment details===
host: YOUTRACK4.agilix.loc
base url: http://youtrack3.agilix.com
version: 3.3
build: 2503 [28-Apr-2012 20:21] 
java.version: 1.6.0_20
java.vendor: Sun Microsystems Inc.
java.vm.specification.version: 1.0
java.vm.specification.vendor: Sun Microsystems Inc.
java.vm.specification.name: Java Virtual Machine Specification
java.vm.version: 16.3-b01
java.vm.vendor: Sun Microsystems Inc.
java.vm.name: Java HotSpot(TM) Server VM
java.specification.version: 1.6
java.specification.vendor: Sun Microsystems Inc.
java.specification.name: Java Platform API Specification
java.class.version: 50.0
os.name: Windows Server 2008 R2
os.arch: x86
os.version: 6.1
Max memory: 1 GB (1520435200 bytes)
Free memory: 204 MB (214691120 bytes)
Total memory: 748 MB (784662528 bytes)
Available processors: 1
Thrown at: Thursday, May 30, 2013 10:14:38 AM MDT

The Java error is:

java.lang.NullPointerException
	at jetbrains.exodus.textindex.impl.HitsEntityIterable.getIteratorUnsafe(HitsEntityIterable.java:50)
	at jetbrains.exodus.textindex.impl.HitsEntityIterable.getIteratorImpl(HitsEntityIterable.java:40)
	at jetbrains.exodus.database.impl.iterate.EntityIterableBase.iterator(EntityIterableBase.java:74)
	at jetbrains.exodus.database.impl.iterate.binop.IntersectionIterable$SortedIterator.<init>(IntersectionIterable.java:78)
	at jetbrains.exodus.database.impl.iterate.binop.IntersectionIterable$SortedIterator.<init>(IntersectionIterable.java:66)
	at jetbrains.exodus.database.impl.iterate.binop.IntersectionIterable.getIteratorImpl(IntersectionIterable.java:52)
	at jetbrains.exodus.database.impl.iterate.binop.IntersectionIterable.getIteratorImpl(IntersectionIterable.java:15)
	at jetbrains.exodus.database.impl.iterate.EntityIterableBase.iterator(EntityIterableBase.java:74)
	at jetbrains.exodus.database.impl.iterate.SkipEntityIterable$1.skip(SkipEntityIterable.java:58)
	at jetbrains.exodus.database.impl.iterate.SkipEntityIterable$1.hasNextImpl(SkipEntityIterable.java:40)
	at jetbrains.exodus.database.impl.iterate.EntityIteratorBase.hasNext(EntityIteratorBase.java:68)
	at jetbrains.exodus.database.impl.iterate.EntityIterableBase.isEmpty(EntityIterableBase.java:92)
	at com.jetbrains.teamsys.dnq.database.PersistentEntityIterableWrapper.isEmpty(PersistentEntityIterableWrapper.java:101)
	at jetbrains.teamsys.dnq.runtime.queries.QueryOperations.isEmpty(QueryOperations.java:289)
	at jetbrains.charisma.smartui.filter.FilterData.getAtLeastResults(FilterData.java:84)
	at jetbrains.charisma.smartui.workspace.Issues_RootHtmlTemplateComponent$11.invoke(Issues_RootHtmlTemplateComponent.java:259)
	at jetbrains.charisma.smartui.workspace.Issues_RootHtmlTemplateComponent$11.invoke(Issues_RootHtmlTemplateComponent.java:256)
	at jetbrains.charisma.smartui.pager.PagerInfo.update(PagerInfo.java:187)
	at jetbrains.charisma.smartui.workspace.Issues_RootHtmlTemplateComponent.onEnter(Issues_RootHtmlTemplateComponent.java:264)
	at jetbrains.mps.webr.runtime.templateComponent.TemplateComponent.<init>(TemplateComponent.java:133)
	at jetbrains.charisma.smartui.workspace.Issues_RootHtmlTemplateComponent.<init>(Issues_RootHtmlTemplateComponent.java:106)
	at jetbrains.charisma.smartui.workspace.Issues_RootHtmlTemplateController$Action.createTemplateComponent(Issues_RootHtmlTemplateController.java:49)
	at jetbrains.mps.webr.runtime.templateComponent.TemplateActionController.getRootTemplateRenderResponseAction(TemplateActionController.java:59)
	at jetbrains.mps.webr.runtime.templateComponent.TemplateActionController.doEnterAction(TemplateActionController.java:37)
	at jetbrains.mps.webr.runtime.templateComponent.ActionController.securedRefreshResponse(ActionController.java:157)
	at jetbrains.mps.webr.runtime.templateComponent.ActionController.enterAction(ActionController.java:84)
	at jetbrains.mps.webr.runtime.requestProcessor.ActionControllerUtil.doEnterAction(ActionControllerUtil.java:17)
	at jetbrains.mps.webr.runtime.requestProcessor.ActionControllerUtil.processRequest(ActionControllerUtil.java:58)
	at jetbrains.mps.webr.runtime.requestProcessor.HtmlTemplateRequestProcessor.processRequest(HtmlTemplateRequestProcessor.java:42)
	at jetbrains.mps.webr.runtime.servlet.MainServlet.processRequest(MainServlet.java:204)
	at jetbrains.mps.webr.runtime.servlet.MainServlet.doGet(MainServlet.java:94)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at jetbrains.mps.webr.runtime.filter.QueryParameterFilter.doFilter(QueryParameterFilter.java:25)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.eclipse.jetty.continuation.ContinuationFilter.doFilter(ContinuationFilter.java:92)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:77)
	at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:133)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
	at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:859)
	at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:579)
	at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1555)
	at java.lang.Thread.run(Unknown Source)

Additionally, I have to restart the Windows service every other day because after one backup process completes successfully, the next one hangs and leaves the system unable to post edits.

I've tried re-applying the Text Index, but it hasn't made a difference.