Here is what I suggest. Take your temp card to another PADI shop and have them use it to look up your cert in the PADI system. If they can't find it, they will probably call PADI to try and get more info. PADI is more likely to talk to one of their 5 stars than an individual diver. If some SB members already handled this part for you, skip it and fast forward... If it turns out there is no record, I'd go back to the shop you trained with and throw all of this info in their face. Doing this might seem odd, but when it comes to disputes with a business, your best chance of getting them resolved is to overwhelm them with facts that are in your favor. Their solution may be something as simple as resubmitting your paperwork under another instructor's number. However, if they do that, I would start to seriously question the quality of your training. If they go that route, I think in the interest of your own safety, you should find another shop or instructor and sign up for a refresher course but also explain the reason why you are signing up, i.e. "I have reason to doubt the quality of my initial training"... Refreshers should not cost much but they will run you through all of the required skills. And, once you explain the situation, any instructor worth his card will likely go above and beyond the basic refresher to help you out as much as possible. Getting your C card is obviously important, but the much more important thing here is to ensure you have the necessary training and skills before diving outside of a training environment. Good luck, let us know how this turns out!
