The webMethods Integration Server Built-In Services document also notes this deprecation. Perhaps you missed this when reviewing the doc during your troubleshooting 
Note:
Because some three-letter abbreviations can represent multiple time zones (for example, “CST”
could represent both U.S. “Central Standard Time” and “China Standard Time”), all abbreviations
are deprecated. Use the full name or custom time zone ID formats instead.
It also notes: “You can use the java.util.TimeZone.getAvailableIDs() method to obtain a list of the valid full name time zone IDs that your JVM version supports.”
You may find EST5EDT and CST6CDT are available in your JVM.
#webMethods#Integration-Server-and-ESB#Service-Designer