Upon further research, I've found that this is not a Windows/Linux issue, rather it's a difference between Java 7 and Java 8. On Java 8, splitting with the empty string no longer produces a sequence that begins with an empty string.
As you said before, this is just a gotcha relating to Java, not a Clojure issue.
Minor
Splitting a string using clojure.string/split with an empty regex includes the empty string in the results - is this expected behaviour?
Example:
user=> (clojure.string/split "abc" #"") ["" "a" "b" "c"]