apicover failed to run if utilized signature file is more narrow (or equal) than API under review in spite of using -tsExclude options.
if Signature file generated as follows:
--Command snippet--
java -client -Xmixed -Xms32m -Xmx192m sigtestdev.jar com.sun.tdk.signaturetest.Setup -keepFile -static -FileName /net/jck/export1/users/lk157052/ws/jck/7/_cover/j2se7_xml.sig -Classpath ... -package javax.jws -package javax.jws.soap -package javax.xml -package javax.xml.bind -package javax.xml.bind.annotation -package javax.xml.bind.annotation.adapters -package javax.xml.bind.attachment -package javax.xml.bind.helpers -package javax.xml.bind.util -package javax.xml.crypto -package javax.xml.crypto.dom -package javax.xml.crypto.dsig -package javax.xml.crypto.dsig.dom -package javax.xml.crypto.dsig.keyinfo -package javax.xml.crypto.dsig.spec -package javax.xml.datatype -package javax.xml.namespace -package javax.xml.parsers -package javax.xml.soap -package javax.xml.stream -package javax.xml.stream.events -package javax.xml.stream.util -package javax.xml.transform -package javax.xml.transform.dom -package javax.xml.transform.sax -package javax.xml.transform.stax -package javax.xml.transform.stream -package javax.xml.validation -package javax.xml.ws -package javax.xml.ws.handler -package javax.xml.ws.handler.soap -package javax.xml.ws.http -package javax.xml.ws.soap -package javax.xml.ws.spi -package javax.xml.xpath -package org.w3c.dom -package org.w3c.dom.bootstrap -package org.w3c.dom.events -package org.w3c.dom.ls -package org.xml.sax -package org.xml.sax.ext -package org.xml.sax.helpers -exclude org.w3c.dom.css \
-exclude org.w3c.dom.html \
-exclude org.w3c.dom.ranges \
-exclude org.w3c.dom.stylesheets \
-exclude org.w3c.dom.traversal \
-exclude org.w3c.dom.views \
-exclude org.w3c.dom.xpath

And for running apicover is used the following command that has the same set of included/exclude packages:
--Command snippet--
java -Xmx512m -cp ... com.sun.tdk.apicover.Main -debug -api j2se7_xml.sig -mode r -format plain -detail 4 -ts JCK-runtime-7-api/classes -report j2se7_xml_api.apc -apiInclude javax.jws -apiInclude javax.jws.soap -apiInclude javax.xml -apiInclude javax.xml.bind -apiInclude javax.xml.bind.annotation -apiInclude javax.xml.bind.annotation.adapters -apiInclude javax.xml.bind.attachment -apiInclude javax.xml.bind.helpers -apiInclude javax.xml.bind.util -apiInclude javax.xml.crypto -apiInclude javax.xml.crypto.dom -apiInclude javax.xml.crypto.dsig -apiInclude javax.xml.crypto.dsig.dom -apiInclude javax.xml.crypto.dsig.keyinfo -apiInclude javax.xml.crypto.dsig.spec -apiInclude javax.xml.datatype -apiInclude javax.xml.namespace -apiInclude javax.xml.parsers -apiInclude javax.xml.soap -apiInclude javax.xml.stream -apiInclude javax.xml.stream.events -apiInclude javax.xml.stream.util -apiInclude javax.xml.transform -apiInclude javax.xml.transform.dom -apiInclude javax.xml.transform.sax -apiInclude javax.xml.transform.stax -apiInclude javax.xml.transform.stream -apiInclude javax.xml.validation -apiInclude javax.xml.ws -apiInclude javax.xml.ws.handler -apiInclude javax.xml.ws.handler.soap -apiInclude javax.xml.ws.http -apiInclude javax.xml.ws.soap -apiInclude javax.xml.ws.spi -apiInclude javax.xml.xpath -apiInclude org.w3c.dom -apiInclude org.w3c.dom.bootstrap -apiInclude org.w3c.dom.events -apiInclude org.w3c.dom.ls -apiInclude org.xml.sax -apiInclude org.xml.sax.ext -apiInclude org.xml.sax.helpers -apiExclude org.w3c.dom.css -apiExclude org.w3c.dom.html -apiExclude org.w3c.dom.ranges -apiExclude org.w3c.dom.stylesheets -apiExclude org.w3c.dom.traversal -apiExclude org.w3c.dom.views -apiExclude org.w3c.dom.xpath -tsInclude javasoft.sqe.tests -tsInclude javasoft.sqe.tests.api -tsInclude javasoft.sqe.tests.api.javax -tsInclude javasoft.sqe.tests.api.org -tsInclude javasoft.sqe.tests.api.xml -tsInclude javasoft.sqe.tests.api.xsl -tsInclude javasoft.sqe.tests.bind
-tsExclude javasoft.sqe.tests.api.java.io.ObjectStreamClass
-tsExclude javasoft.sqe.tests.vm
-tsExclude javasoft.sqe.tests.lang
-tsExclude javasoft.sqe.tests.api.java
-tsExclude javasoft.sqe.tests.api.java.security
-tsExclude javasoft.sqe.tests.api.java.security.cert

then apicover fails with stacktrace:
java.lang.ClassNotFoundException: org.w3c.dom.traversal.NodeFilter
        at com.sun.tdk.signaturetest.loaders.VirtualClassDescriptionLoader.load(VirtualClassDescriptionLoader.java:57)
        at com.sun.tdk.signaturetest.core.ClassHierarchyImpl.load(ClassHierarchyImpl.java:180)
        at com.sun.tdk.signaturetest.core.ClassHierarchyImpl.load(ClassHierarchyImpl.java:164)
        at com.sun.tdk.signaturetest.core.MemberCollectionBuilder.getMembers(MemberCollectionBuilder.java:250)
        at com.sun.tdk.signaturetest.core.MemberCollectionBuilder.getMembers(MemberCollectionBuilder.java:117)
        at com.sun.tdk.signaturetest.core.MemberCollectionBuilder.createMembers(MemberCollectionBuilder.java:72)
        at com.sun.tdk.apicover.Main.check(Main.java:382)
        at com.sun.tdk.apicover.Main.run(Main.java:147)
        at com.sun.tdk.apicover.Main.main(Main.java:132)
Unexpected exception during check org.w3c.dom.traversal.NodeFilter

If apicover starts without -tsExclude options the failure stack is the same as above.