The most common culprit is an anti-virus program, with "on-the-fly" file checking enabled - i.e. whenever a file is opened and / or written to it gets virus checked.
Example - combine that with java apps - the java run-time environment is a MINIMUM of 50 MB - and you get a fairly lengthy pause while AV runs.
To try to identify what is taking 100% CPU, load Task Manager (ctrl alt del), and keep it in the background; then when the computer freezes, see what process is consuming the CPU cycles.
SD