It may have had something to do with the Google Reader shutdown. The reason I say this, is that I just recently launched an RSSOwl instance, where I had populated RSSOwl with a list of feeds some time ago... including quite a few Google Alert RSS feeds. Strangely none of the Google Alerts were working, and when I started investigating, I found that all of them had a path that included something like

$BLAH/reader/$BLAH

which suggests that, when those feeds were originally created, the delivery mechanism somehow involved GReader.

I went back to Google Alerts and re-copied each of the feed URLs and see that in the new URLs, the path looks like:

$BLAH/alerts/$BLAH

Not definitive, but it hints at some kind of connection.