IntelliJ performance issues Follow

Hey everyone,
So I switched to IntelliJ a few months ago and now have some experience with it. I'm having really annoying performance issues. Sometimes it would just get stuck for 10-20 seconds without giving any indication that it's actualyl doing anything. Sometimes it slows down for indexing, sometimes it'll slow down because of re-importing POMs (That happens after updating files from the source control), see a previous post about that http://devnet.jetbrains.net/thread/293725?tstart=0 (Still no resolution).
I have no idea how to address these issues, is there a log for IntelliJ I may turn on? I noticed the log.xml file under the bin directory, what can I do with it to isolate the problem?

I work on a large project that has about 130 modules. It's POM based and contains both Java and Flex projects. The product version I'm using is 9.0.4.

Here's what I've tried so far:

1. Changing the skin to 4.5
2. Defragging the hard drive
3. Removing any unused plug-ins

I also read someone who said the "Project" view might cause performance problems and switch to "Modules" view, but that is one of the best features of this product so I don't want to do that.

I would appreciate any help.

Guy Marom