Hi Jacde,
I've had the same problem, ended up just running my cases in smaller batches as a "quick fix". Otherwise, the resulting output had alot of ripples in them and unstable starting conditions (during steady state before trip). However, I'd be very interested in hearing an answer on this subject if anyone has it.
My script is a three layered loop running all the combinations of the data file types and specified contingencies (.sav, .dyr and then specified line-trips) with each file type having approximately 8 files. I also noticed that when running the same script with the same number of cases/contingencies/dynamic data files using the example file savnw I did not get the same problem, however the .sav-file I am using for my simulations are >200 times in terms of kB.
I've sent the question forward to PTI Support but they have been unable to answer. Sorry I cannot be of more help, anyone else here with an answer to this?