I figured it out and it was all my fault. I'll explain in detail in case someone else has a similar problem:
I am using APC on my server and had enabled this variable:
apc.stat
this is its definition:
Be careful changing this setting. This defaults to on, forcing APC to stat (check) the script on each request to determine if it has been modified. If it has been modified it will recompile and cache the new version. If this setting is off, APC will not check, which usually means that to force APC to recheck files, the web server will have to be restarted or the cache will have to be manually cleared. Note that FastCGI web server configurations may not clear the cache on restart. On a production server where the script files rarely change, a significant performance boost can be achieved by disabled stats.
For included/required files this option applies as well, but note that for relative path includes (any path that doesn't start with / on Unix) APC has to check in order to uniquely identify the file. If you use absolute path includes APC can skip the stat and use that absolute path as the unique identifier for the file.
I had disabled checking for changed scripts since all apc ttl settings on this particular site are set to 1h and nothing much changes except for plugin updates of course. Once I emptied the opcode cache everything was good :-)
@treydock: it was you who was maintaining that modified wpmu bad behavior version, wasn't it? Is there any way of subscribing to news and updates about it?
treydock