Anytime a particular test run involves running several commands the output of the last command overwrites the previous ones. This is caused by passing around the log file as a File inside partest and opening the log file in truncate mode.
Just an example: this causes all warnings to be ignored in test/files/run tests because the output of the test overwrites the output from scalac.
A related issue is that by default test/partest runs all test with "-deprecation" option while the ant and sbt runners use no option. AFAIK currently it does not make any difference but if this bug is fixed, the test outputs will differ.
You can find the WIP fix including the changes needed to *.check files: https://github.com/khernyo/scala/commits/unstable/issue/7003. This is mixed up with a WIP fix for
SI-6289 which I will clean up later.