Acrobat Pro XI v.11.0.06 - PDF created by Microstation Print Organizer - Windows 7 -  Printing shaded squares on top of shaded building and not displayed on screen, only displays on paper when printing

I have attached an image of the sheet to show the areas that are shaded. The building is supposed to be shaded, however the two squares within are not. These squares are not in the file converted to pdf and do not display on screen when viewing the pdf. Also there are several sheets in the set with shaded buildings and only two of the buildings have this issue. Any help with this would be greatly appreciated.

I'm seeing this same problem happen on multiple platforms here in the office. Every time this happens, the screen view does not show these shapes. I have been seeing the same problem except linework will be missing in one of these square shapes as well. Please give feedback if anyone knows what causes this problem. One thing to note -  these squares are the size and placement of a selection box within acrobat.  For example, if i use the selection tool and click near where the problem printed out, the shaded area that gets selected is in the exact same spot and is the exact size.@

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    2009-07-02 12:19:25,241 INFO  [com.adobe.pdfg.BMCCaller] ALC-PDG-001-028-FORMUlÀRIO DE HORA EXTRA.doc: Job Completion Status: Failed
    2009-07-02 12:19:25,241 INFO  [com.adobe.pdfg.BMCCaller] ALC-PDG-001-025-FORMUlÀRIO DE HORA EXTRA.doc: Time Job Completed: 02/07/09 12:19
    2009-07-02 12:19:25,241 INFO  [com.adobe.pdfg.BMCCaller] ALC-PDG-001-026-FORMUlÀRIO DE HORA EXTRA.doc: Time of Job Execution: 379.486 ms
    2009-07-02 12:19:25,241 ERROR [com.adobe.pdfg.GeneratePDFImpl] ALC-PDG-001-000-ALC-PDG-010-015-The conversion operation timed out before it could be completed. Please report this error to the system administrator.
    2009-07-02 12:19:25,241 ERROR [com.adobe.aes.web.create.CreatePDFAct] ALC-PDG-001-000-Invocation error.
    ALC-DSC-003-000: com.adobe.idp.dsc.DSCInvocationException: Invocation error.
    at com.adobe.idp.dsc.component.impl.DefaultPOJOInvokerImpl.invoke(DefaultPOJOInvokerImpl.jav a:152)
    at com.adobe.idp.dsc.interceptor.impl.InvocationInterceptor.intercept(InvocationInterceptor. java:140)
    at com.adobe.idp.dsc.interceptor.impl.RequestInterceptorChainImpl.proceed(RequestInterceptor ChainImpl.java:60)
    at com.adobe.idp.dsc.transaction.interceptor.TransactionInterceptor$1.doInTransaction(Transa ctionInterceptor.java:74)
    at com.adobe.idp.dsc.transaction.impl.ejb.adapter.EjbTransactionBMTAdapterBean.doBMT(EjbTran sactionBMTAdapterBean.java:197)
    at sun.reflect.GeneratedMethodAccessor358.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:585)
    at org.jboss.invocation.Invocation.performCall(Invocation.java:345)
    at org.jboss.ejb.StatelessSessionContainer$ContainerInterceptor.invoke(StatelessSessionConta iner.java:214)
    at org.jboss.resource.connectionmanager.CachedConnectionInterceptor.invoke(CachedConnectionI nterceptor.java:149)
    at org.jboss.webservice.server.ServiceEndpointInterceptor.invoke(ServiceEndpointInterceptor. java:54)
    at org.jboss.ejb.plugins.CallValidationInterceptor.invoke(CallValidationInterceptor.java:48)
    at org.jboss.ejb.plugins.AbstractTxInterceptor.invokeNext(AbstractTxInterceptor.java:106)
    at org.jboss.ejb.plugins.AbstractTxInterceptorBMT.invokeNext(AbstractTxInterceptorBMT.java:1 58)
    at org.jboss.ejb.plugins.TxInterceptorBMT.invoke(TxInterceptorBMT.java:62)
    at org.jboss.ejb.plugins.StatelessSessionInstanceInterceptor.invoke(StatelessSessionInstance Interceptor.java:154)
    at org.jboss.ejb.plugins.SecurityInterceptor.invoke(SecurityInterceptor.java:153)
    at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:192)
    at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor. java:122)
    at org.jboss.ejb.SessionContainer.internalInvoke(SessionContainer.java:624)
    at org.jboss.ejb.Container.invoke(Container.java:873)
    at org.jboss.ejb.plugins.local.BaseLocalProxyFactory.invoke(BaseLocalProxyFactory.java:415)
    at org.jboss.ejb.plugins.local.StatelessSessionProxy.invoke(StatelessSessionProxy.java:88)
    at $Proxy160.doBMT(Unknown Source)
    at com.adobe.idp.dsc.transaction.impl.ejb.EjbTransactionProvider.execute(EjbTransactionProvi der.java:95)
    at com.adobe.idp.dsc.transaction.interceptor.TransactionInterceptor.intercept(TransactionInt erceptor.java:72)
    at com.adobe.idp.dsc.interceptor.impl.RequestInterceptorChainImpl.proceed(RequestInterceptor ChainImpl.java:60)
    at com.adobe.idp.dsc.interceptor.impl.InvocationStrategyInterceptor.intercept(InvocationStra tegyInterceptor.java:55)
    at com.adobe.idp.dsc.interceptor.impl.RequestInterceptorChainImpl.proceed(RequestInterceptor ChainImpl.java:60)
    at com.adobe.idp.dsc.interceptor.impl.InvalidStateInterceptor.intercept(InvalidStateIntercep tor.java:37)
    at com.adobe.idp.dsc.interceptor.impl.RequestInterceptorChainImpl.proceed(RequestInterceptor ChainImpl.java:60)
    at com.adobe.idp.dsc.interceptor.impl.AuthorizationInterceptor.intercept(AuthorizationInterc eptor.java:132)
    at com.adobe.idp.dsc.interceptor.impl.RequestInterceptorChainImpl.proceed(RequestInterceptor ChainImpl.java:60)
    at com.adobe.idp.dsc.interceptor.impl.JMXInterceptor.intercept(JMXInterceptor.java:48)
    at com.adobe.idp.dsc.interceptor.impl.RequestInterceptorChainImpl.proceed(RequestInterceptor ChainImpl.java:60)
    at com.adobe.idp.dsc.engine.impl.ServiceEngineImpl.invoke(ServiceEngineImpl.java:115)
    at com.adobe.idp.dsc.routing.Router.routeRequest(Router.java:118)
    at com.adobe.idp.dsc.provider.impl.base.AbstractMessageReceiver.routeMessage(AbstractMessage Receiver.java:91)
    at com.adobe.idp.dsc.provider.impl.vm.VMMessageDispatcher.doSend(VMMessageDispatcher.java:21 5)
    at com.adobe.idp.dsc.provider.impl.base.AbstractMessageDispatcher.send(AbstractMessageDispat cher.java:57)
    at com.adobe.idp.dsc.clientsdk.ServiceClient.invoke(ServiceClient.java:208)
    at com.adobe.aes.web.create.CreatePDFAct.createPDF(CreatePDFAct.java:383)
    at com.adobe.aes.web.create.CreatePDFAct.createPDF2(CreatePDFAct.java:402)
    at com.adobe.aes.web.create.CreatePDFAct.execute(CreatePDFAct.java:174)
    at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:431)
    at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:236)
    at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1196)
    at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:432)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    at com.adobe.aes.web.AesActionServlet.service(AesActionServlet.java:63)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:810)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.j ava:252)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
    at com.adobe.idp.um.auth.filter.AuthenticationFilter.doFilter(AuthenticationFilter.java:154)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.j ava:202)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
    at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:81)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.j ava:202)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
    at org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalValve.java:39)
    at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.ja va:159)
    at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:59)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11P rotocol.java:744)
    at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
    at org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThread.java:112)
    at java.lang.Thread.run(Thread.java:595)
    Caused by: ALC-PDG-10015-000: com.adobe.livecycle.generatepdf.client.ConversionException: ALC-PDG-010-015-The conversion operation timed out before it could be completed. Please report this error to the system administrator.
    at com.adobe.pdfg.BMCCaller.checkResult(BMCCaller.java:358)
    at com.adobe.pdfg.Native2PdfCaller.callNativeBMC(Native2PdfCaller.java:788)
    at com.adobe.pdfg.Native2PdfCaller.createPDF(Native2PdfCaller.java:298)
    at com.adobe.pdfg.GeneratePDFImpl.createPDFCommon(GeneratePDFImpl.java:342)
    at com.adobe.pdfg.GeneratePDFImpl.createPDF(GeneratePDFImpl.java:172)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:585)
    at com.adobe.idp.dsc.component.impl.DefaultPOJOInvokerImpl.invoke(DefaultPOJOInvokerImpl.jav a:118)
    ... 73 more

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