Hi gaya,
If I understand your problem correctly, you can't figure out why you are getting the waveforms are not contiguous error. One thing I would suggest is to take a look at this KnowledgeBase which talks about using the Align and Resample Express VI and talks about which acquisition type to use:
Unfortunately I cannot run your VI because I don't have the HP546XXX set of VIs installed. Could you possibly either cut this VI down to not use them by simulating data so that I could test it out?
Another option you might want to try is to have the dt user input earlier on in the VI so that you don't have to use this express VI. I'm not sure if this is possible again since I can't see the exact set of VIs you are using.
The root cause of this might be because of the time delay you have in your loop. The readings aren't contiguous because you are reading ever half second apart. Try removing the delay and see if that gets rid of the error.
I hope some of this helped! Please let me know if none of this did and what you tried and repost the code if possible. Thanks!
~Stephanie