Hi mattwilko,
I believe the first issue that you should address is the building of arrays.
This is mainly happening on the edge of your loops.
This is my reasoning.
Allocating memory in RT to handle an array that is growing will blow away your determinism.
I would suggets pre-allocating all of your storage and work with the data in-place.
In LV 7.1 there are some great new tools that will help nail down issue of this type.
If you have LV 7.1 you may want to upgrade so you can take advantage of the new tools.
Trying to help,
Ben