If you use ProcessTools.startProcess() and apply an OutputAnalyzer right afterwards as shown below:

            p = ProcessTools.startProcess("java", pb);
            out = new OutputAnalyzer(p);

Some of the output will end up with the OutputAnalyzer, and some automatically included in the .jtr file with the "[java]" prefix. It seems to be randomly divvied up between the two, whereas all the output should appear in both.

Using the Consumer argument has a similar issue:

            p = ProcessTools.startProcess("java", pb, outputConsumer);
            out = new OutputAnalyzer(p);

The lines that are directed to the Consumer are the same as the lines you see with the "[java]" prefix. The rest are directed to the OutputAnalyzer. The issue happens with both stdout and stderr.

Please see the attached test case. It runs once with without a consumer and once with. I'm not certain you will always see both test cases fail on all processors since some of it might be timing related. For example, without a consumer I see:

[2019-11-06T00:42:06.891310Z] Gathering output for process 27274
DEBUG: process started.
[java] A line on stdout 0
FAILED: wrong number of lines in OutputAnalyzer output
DEBUG: OutputAnalyzer output: got 49 lines, expected 50. Output follows:
A line on stdout 1
A line on stdout 2
<...>

So only the first line ended up with the "[java]" prefix. If it had instead ended up in the OutputAnalyzer output, the test would not have detected any failures because it can't actually see that were no lines of "[java]" output.

The Consumer case which runs second seems to do a much better job of showing this issue, at least when run on my machine:

[2019-11-06T00:42:06.923088Z] Gathering output for process 27297
DEBUG: process started.
[java] A line on stdout 0
[java] A line on stdout 26
[java] A line on stdout 30
[java] A line on stdout 33
[java] A line on stdout 35
[java] A line on stdout 37
[java] A line on stdout 39
[java] A line on stdout 42
[java] A line on stdout 44
[java] A line on stdout 47
[java] A line on stdout 49
FAILED: wrong number of lines in Consumer output
DEBUG: Consumer output: got 11 lines, expected 50. Output follow:
A line on stdout 0
A line on stdout 26
A line on stdout 30
A line on stdout 33
A line on stdout 35
A line on stdout 37
A line on stdout 39
A line on stdout 42
A line on stdout 44
A line on stdout 47
A line on stdout 49
DEBUG: done with Consumer output.
FAILED: wrong number of lines in OutputAnalyzer output
DEBUG: OutputAnalyzer output: got 39 lines, expected 50. Output follows:
A line on stdout 1
A line on stdout 2
<...>
A line on stdout 24
A line on stdout 25
A line on stdout 27
A line on stdout 28
A line on stdout 29
A line on stdout 31
A line on stdout 32
A line on stdout 34
A line on stdout 36
A line on stdout 38
A line on stdout 40
A line on stdout 41
A line on stdout 43
A line on stdout 45
A line on stdout 46
A line on stdout 48

So in this case here were 11 lines, scattered from throughout the output, that appeared with the "[java]" prefix and also with the Consumer. The rest were in the OutputAnalyzer.