Apparently along with the changes on how the database queries are caching to disk, @Frederick also made changes on how the pages are caching to disk.
That certainly made some problems with the page caching and probably the cron job, at least in some environments. So this is what is happening:
1. When caching pages to disc (basic), W3TC fails to even serve the cached pages. Time-stamps change on every single visit. The pages are created on disc, but not served.
2. When caching pages to disc (enhanced), W3TC fails to collect the garbage and refresh the pages at specified intervals. Time-stamps remain the same long after the collect garbage interval have passed. After some testing I'm assuming that what is happening is that W3TC is taking into account the caching intervals from the database caching, page caching, and browser html caching cumulatively.
When setting page cache (enhanced) to expire let say at 300, the cache will be gone at 600-700, depending on what I have set for the database and browser caching.
