There are several people with similar issues in relation to mintUpdate. I have found that if I click the "refresh" button, the updates will appear. Not sure what the exact problem is, but there have been several threads about this behavior. I just give it an extra click, and all is then well again.
As an aside, while you are reading through threads, you may also see posts about some who do wholesale updates in Synaptic having problems. It is safer to use mintUpdate with Level 1, 2, and 3 updates. Ultimately, you must decide what is the best method for your machine. Good luck.