Either memory allocation or a non-deterministic OS could cause the jitter you are seeing. Most likely, you would see this behavior anytime when running on a non-deterministic OS, regardless of whether you are performing memory allocations, but this effect would be exacerbated by performing memory allocations. Also, memory allocations can introduce jitter even when running on a real-time OS. Thus, to completely eliminate this problem, you will have to move to a real-time platform (such as LabVIEW RT) as well as eliminate any memory allocations inside your loop.
Best of luck,
Joe