Here's a fairly serious related issue, which I'm fixing. I don't know how this would explain it in the context of jenkins runs though, since there's no reason it should be receiving the same tests with differently constructed paths. But,
No no partest, that's one test, written three ways!
% test/partest test/files/run/freetypes_false_alarm1.scala \
./test/files/run/freetypes_false_alarm1.scala \
/scala/trunk/test/files/run/freetypes_false_alarm1.scala
Selected 3 tests drawn from specified tests
# starting 3 tests in run
ok 1 - run/freetypes_false_alarm1.scala
Uncaught exception on thread Thread[main,5,main]: java.lang.RuntimeException: Error running ./test/files/run/freetypes_false_alarm1.scala
java.lang.RuntimeException: Error running ./test/files/run/freetypes_false_alarm1.scala
at scala.tools.partest.nest.RunnerManager.liftedTree1$1(Runner.scala:825)
at scala.tools.partest.nest.RunnerManager.runTest(Runner.scala:823)
at scala.tools.partest.nest.DirectRunner$$anonfun$22$$anonfun$apply$6.apply(Runner.scala:727)