Yes, you should upgrade either to 5.005_03 or 5.6.1. Which one depends on how many local dependencies you have and how much energy for testing. (If you have to bite the bullet, 5.6.1 would be better, but going to it is also inherently more risky.)

I have long ago blissfully forgotten the details, but 5.005_02 had at least one bug which lead to infinite loops. An unexpected infinite loop in which you are tying up memory would show up as an out of memory issue.

So I cannot guarantee you that an upgrade would solve your problem, but it sounds to me like a pretty good bet.