Tricky question.

Try lowering the engine's priority:

Are you sure it's the latest edition of Houdini 1.5?

I had the same problem with the 1st version, it had a known bug.

Anyway, using 99% CPU is a good thing. Chess engines are programs that want to calculate as much as they possibly can and are supposed to keep the CPU occupied all of the time.

But the user interface should have a higher priority, so that you can still do things.

If your processor is multi-core, you can limit the number of cores houdini uses. This will prevent hanging and allow you to do other tasks without hangups. The problem is you actually want to use as much of the cpu as you can for houdini, so you pretty much have to let it hang if you want the best analysis in the quickest available time.

An ideal setup for advanced chess is to use a laptop for online interface, while using a desktop for entering moves into the chess software. That way you get 100% core usage and are still able to navigate the web site without delay.