After installing BC 6.3 and starting the Interior server, the following error is thrown.
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2017 Aug 10 12:52:08:004 GMT -0400 BW.BusinessConnect-Interior_Server Error [bw.logger] BW-EXT-LOG-100000  com.tibco.ax.fw.util.BCSecurityException
    at com.tibco.ax.fw.util.MiscUtil.decodeSecret(MiscUtil.java:652)
    at com.tibco.ax.fw.impl.om.OmJdbcInfo.getPasswordAsString(OmJdbcInfo.java:82)
    at com.tibco.ax.fw.db.DbTableMetaCache.init(DbTableMetaCache.java:77)
    at com.tibco.ax.fw.db.DbTableMetaCache.init(DbTableMetaCache.java:40)
    at com.tibco.ax.fw.runtime.impl.RuntimeBootstrap.sInit(RuntimeBootstrap.java:413)
    at com.tibco.ax.fw.runtime.impl.RuntimeBootstrap.sInit(RuntimeBootstrap.java:170)
    at com.tibco.plugin.gateway.GatewayBootstrap.init(GatewayBootstrap.java:38)
    at com.tibco.plugin.gateway.GatewayBootstrap.<init>(GatewayBootstrap.java:32)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at com.tibco.ae.processapi.ui.javachooser.JavaClassMethodUtility.createNewInstance(Unknown Source)
    at com.tibco.plugin.java.JavaGlobalServiceAgent.for(Unknown Source)
    at com.tibco.plugin.java.JavaGlobalServiceAgent.init(Unknown Source)
    at com.tibco.pe.core.AgentJobCreator.init(Unknown Source)
    at com.tibco.pe.core.JobPoolConfigurator.do(Unknown Source)
    at com.tibco.pe.core.JobPoolConfigurator.a(Unknown Source)
    at com.tibco.pe.core.FTActivator.itsTime(Unknown Source)
    at com.tibco.pe.util.ReminderQueue.run(Unknown Source)
Caused by: java.lang.IllegalArgumentException: invalid Base-64 encoded string
    at com.tibco.security.impl.B.F.new(Base64.java:125)
    at com.tibco.security.Crypto.undo(Crypto.java:73)
    at com.tibco.ax.fw.util.RenameTextFile.undo(RenameTextFile.java:36)
    at com.tibco.ax.fw.util.RenameTextFile.undo(RenameTextFile.java:41)
    at com.tibco.ax.fw.util.KSUtil.unObfuscate(KSUtil.java:56)
    at com.tibco.ax.fw.crypto.InitCiphers.unObfuscate(InitCiphers.java:81)
    at com.tibco.ax.fw.util.MiscUtil.decodeSecret(MiscUtil.java:648)
    ... 19 more
 2017 Aug 10 12:52:08:004 GMT -0400 BW.BusinessConnect-Interior_Server Error [bw.logger] BW-EXT-LOG-100001  ***** Runtime Engine Initialization FAILED 
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This error is generally seen for all password fields such as the JMS and database configuration.

After upgrading to BusinessConnect 6.3.0, the following exception is thrown when starting the BC engine: "java.lang.IllegalArgumentException: invalid Base-64 encoded string"

BC 6.3

Installing BusinessConnect 6.3 hotfix 2 or later will resolve this issue.