The ISAPI verision of PHP is a "run once" module for IIS. The CGI version is completely external to IIS and is run each time a PHP file must be parsed.
Many of the problems with the PHP/ISAPI module to bad behavior within IIS code.
I use the ISAPI module regularly, and I do rarely have IIS crashes when accessing PHP pages. Because the source is not available, the PHP coders can only conform to the published ISAPI specifications (which I'm sure they have to the best of their ability).