Firstly, let me say that this is a great plugin, especially for the terminally paranoid!
I have been using FMP for a while on several sites and recently created a fresh site with WP 3.5. FMP manual scans all files as normal but did not seem to be emailing after changes.
I thought perhaps this was a conflict with something else and left the issue while I finished the site. However, I recently upgraded a couple of other site that already had FMP working perfectly on them and they both stopped emailing updates after the change to 3.5. No other plugin changes.
I was wondering if anyone else had this issue? I noticed Scott said that things were working OK on 3.5 but I cannot get mine to email using the Word Press Cron option as normal. Manual scan still functions as normal (and emails a copy afterwards!)
Thanks in advance!