Data point:

Once upon a time, to study the performance of square versus jagged arrays in .NET I ported to C# the source code of one of the benchmarks mentioned in the article "The NINJA project. CACM 44(10): 102-109 (2001)."

I dug it out today and ran it against the latest version of Microsoft's C# (7.10.3052.4), Mono (Release 0.25, June 25, 2003), and ran the Java version against J# (7.10.3052.0) and Java (1.4.2). I ran each test 3 times on a Motion Computer M1200 Tablet Computer (Mobile P3, 866MHz, 512MB RAM). Timing is done on either side of a function call, so this should not reflect differences in VM start-up time. Results in milliseconds: