I updated to the latest Orion and NPM versions more then a month ago and I also use Alert Central for sending email alerts. I have not seen any issues with alerts not being sent. I am not sure what you mean when you say that you "currently have all my alerts set up in Alert Central." Are you referring to the alert routing to specific groups? The alerts should be configured on your SolarWinds platform (either built-in or custom alerts) and any triggered alert sent between the SolarWinds platform and the Alert Central server using their API connection.
Either way, I have not had any issues. I have the last version of Alert Central they released, which is 184.108.40.2060.
it could be with the subscriptions? perhaps add it and remove the solarwinds source from alert central?