random 1-2sec freezes, in new world (1.4.2) "single player mode", no mods.
On freeze: java occupie 100% CPU usage at all 8 Logical cores.

following message in console:
"WARNING: Can't keep up! Did the system time change, or is the server overloaded?"

Seems related to un-allocating of memory.(According to F3 Debug information), (might be an issue with GC?)

UPDATE:
Configured java arguments manually so that "-Xmx4096M -Xms4096M", problem still persist, so it's not related to java memory allocation changes.

Also tried with OpenJRE 1.7, with no change.

No related messages in syslog.

appending bug description:
if it freezes while "Minecraft Music" is playing; when freeze ends the music does not continue to play.

UPDATE 2:

Ok, so it may be a memory leak, chunk unloading or something wrong with garbage collecting,

Before freeze, memory usage builds up from around ~400MB to >1050-1500MB of total the total 3500ish MB, then it freezes for 1-2 secounds and jumps down to ~400MB.