Well, after tinkering and trying the suggestions from Jeff and this support page (http://digital.ni.com/public.nsf/allkb/A67CA6B0E287081186256D1F0059F40D), I've come to a temporary solution to my problem.
I now merge the DDTs from my DAQ assistant into 1 and convert my SPL scalar value to DDT separately. Then these two lines go through the align and resample ExpressVI. These are then merged before being written to file.
Note: This issue turned out not to be related to the application builder. The 20333 error was intermittently thrown in both the built application and the VI, I just only noticed it in the built application at first.
Another note: While using dynamic data and express VIs are very convenient, they are difficult to debug. I may end up replacing them with the usual DAQmx setup.
