We need to focus on what can be done at this crucial phase due to the nick of time which you have. Did you attempt to make payment of the RPRF online anytime recently? What does the system show?
If it enbles to make payment for you both, then theres nothing to worry about, especially since this amount is refundable. If you are unable to make payment for 2 people due to system option constraints, then what I would advise is that, you go ahead and make payment for the principal applicant, then without any further hold up, raise a CSE, apply for GCSM notes , contact the CIC agent and try gaining information to know the actual reason.
Ask the agent about your (principal applicant) eligibility status, backgroundcheck, security check and then enquire next about the eligibility status, background and security check for your wife (dependent).
Depending on the feedback and with the visibility of whats happening behind the curtains, you can take your required course of action further ahead. Do keep us updated on your status.
Bro, its my request to you to kindly update ur timeline, stream and nationality in your signature, it makes future refernces easier for everyone including yourself.