You have 3 issues:
1) The TRANSFORM messages are a known issue: http://docs.splunk.com/Documentation/WAS/latest/ReleaseNotes/Knownissues . In short: edit props.conf in the default directory and change all words TRANSFORM to TRANSFORMS. Then restart Splunk.
2) indexes and inputs configurations are not internally consistent: some apps contain indexes.conf, depending if you created an index while you started from some of those apps. If you upgraded to 6.1, move all entries from gettingstarted/local/indexes.conf to another app. Then restart Splunk.
3) Regex issue: also in default/props.conf, change the word websphere_DumpRoutineSubComponents (34 characters) to something smaller. It seems the field is not used in any search of the app and I guess you're not going to index javacore files. The field is probably some preparation for some search/view in the future.
Erwin
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