I encourage you to submit the application. Don't be left wondering "what if" at the end of the cycle because there was a mishap with the secondary.
If your cycle goes similarly to how mine went, you will encounter several frustrations with admissions staff. Sending a check will be minor.
Yeah I understand where your coming from, but what I've learned about that "what if" feeling is that it can also just as easily lead you to a place that your gut told you not to go. However, I've become slightly neurotic going through this application process and might end up submitting anyway...