Resolution:
The full text of the error message is below.

The cause of this is the tra.properties file having an incorrect value for 'config.bin_ext='.  The correct setting is 'config.bin_ext=""'.  The error message of "java.lang.StringIndexOutOfBoundsException: String index out of range: 0" gives a hint that some value was not filled in.

The full tra.properties file which worked to generate bpm*.tra is:
__________________________________________________

config.jvmlib=/home/usrglobal/jdk/solaris/j2sdk1.4.2_05/jre/lib/sparc/client/libjvm.so
config.jdk_home=/home/usrglobal/jdk/solaris/java1.4/jre
config.ic_home=/home/dannyboy/tibco/server/dan_bpm201ls125mar8a
config.im_home=/home/dannyboy/tibco/im/5.0
config.ic_shared=/home/dannyboy/tibco/IC71apps/icapps/shared
config.seperator=;
config.bpm_home=/home/dannyboy/tibco/bpmapps/bpmd
config.bin_ext=
config.tibrv_home=/home/netapp1/guy/Tibco/tibrv/8.1
config.icjava_dir=/home/dannyboy/tibco/IC71apps/icapps/shared/java

_______________________________________________________

guy{icadmin}33: !28
/home/dannyboy/tibco/tpcl/5.1/ant/bin/ant
Buildfile: build.xml

GenerateTRAs:

templateGen:
     [copy] Copying 1 file to /home/dannyboy/tibco/bpmapps/bpmd/bin

BUILD FAILED
java.lang.StringIndexOutOfBoundsException: String index out of range: 0
        at java.lang.String.charAt(String.java:444)
        at
org.apache.tools.ant.filters.ReplaceTokens.read(ReplaceTokens.java:160)
        at
org.apache.tools.ant.filters.ReplaceTokens.read(ReplaceTokens.java:196)
        at
org.apache.tools.ant.filters.BaseFilterReader.read(BaseFilterReader.java:123)
        at java.io.BufferedReader.fill(BufferedReader.java:136)
        at java.io.BufferedReader.readLine(BufferedReader.java:299)
        at java.io.BufferedReader.readLine(BufferedReader.java:362)
        at org.apache.tools.ant.util.FileUtils.copyFile(FileUtils.java:367)
        at org.apache.tools.ant.util.FileUtils.copyFile(FileUtils.java:225)
        at org.apache.tools.ant.taskdefs.Copy.doFileOperations(Copy.java:528)
        at org.apache.tools.ant.taskdefs.Copy.execute(Copy.java:369)
        at org.apache.tools.ant.Task.perform(Task.java:341)
        at org.apache.tools.ant.Target.execute(Target.java:309)
        at org.apache.tools.ant.Target.performTasks(Target.java:336)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1339)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:397)
        at org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:143)
        at org.apache.tools.ant.Task.perform(Task.java:341)
        at org.apache.tools.ant.Target.execute(Target.java:309)
        at org.apache.tools.ant.Target.performTasks(Target.java:336)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1339)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1255)
        at org.apache.tools.ant.Main.runBuild(Main.java:609)
        at org.apache.tools.ant.Main.start(Main.java:196)
        at org.apache.tools.ant.Main.main(Main.java:235)

Total time: 4 seconds
java.lang.StringIndexOutOfBoundsException: String index out of range: 0
        at java.lang.String.charAt(String.java:444)
        at
org.apache.tools.ant.filters.ReplaceTokens.read(ReplaceTokens.java:160)
        at
org.apache.tools.ant.filters.ReplaceTokens.read(ReplaceTokens.java:196)
        at
org.apache.tools.ant.filters.BaseFilterReader.read(BaseFilterReader.java:123)
        at java.io.BufferedReader.fill(BufferedReader.java:136)
        at java.io.BufferedReader.readLine(BufferedReader.java:299)
        at java.io.BufferedReader.readLine(BufferedReader.java:362)
        at org.apache.tools.ant.util.FileUtils.copyFile(FileUtils.java:367)
        at org.apache.tools.ant.util.FileUtils.copyFile(FileUtils.java:225)
        at org.apache.tools.ant.taskdefs.Copy.doFileOperations(Copy.java:528)
        at org.apache.tools.ant.taskdefs.Copy.execute(Copy.java:369)
        at org.apache.tools.ant.Task.perform(Task.java:341)
        at org.apache.tools.ant.Target.execute(Target.java:309)
        at org.apache.tools.ant.Target.performTasks(Target.java:336)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1339)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:397)
        at org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:143)
        at org.apache.tools.ant.Task.perform(Task.java:341)
        at org.apache.tools.ant.Target.execute(Target.java:309)
        at org.apache.tools.ant.Target.performTasks(Target.java:336)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1339)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1255)
        at org.apache.tools.ant.Main.runBuild(Main.java:609)
        at org.apache.tools.ant.Main.start(Main.java:196)
        at org.apache.tools.ant.Main.main(Main.java:235)
String index out of range: 0

The generating of the bpm*.tra files with ant on UNIX fails with "BUILD FAILEDjava.lang.StringIndexOutOfBoundsException: String index out of range: 0"