Did you check the MODX date_timezone System Setting to make sure it matches?
You didn't jump all the way from 2.2 to the current version right? You should install all the x.x.0 versions on the way (2.3.0, 2.4.0, 2.5.0, 2.6.0, then the current version).
The hacks have been remarkably persistent. All it takes is one remaining file that the hacker can use to gain entrance again, or even if it doesn't present a vulnerability, it may still crap up the site when it executes. That said, your symptoms don't look like the result of hacking to me (I could be wrong).
SiteCheck, BTW, checks for mismatches in the date/timezone settings and a lot of other things that can cause problems.