FogBugz was originally an internal tool meant to facilitate writing Fog Creek's original first product (CityDesk, a CMS). It seems pretty reasonable to go with whatever's most comfortable for an internal tool that you don't expect to sell, let alone to have different people running on different OSes.
That is to say, it seems like they did choose the better technology stack for the job at hand. If you're going that direction, the real problems started when Joel got a job at Microsoft.
That is to say, it seems like they did choose the better technology stack for the job at hand. If you're going that direction, the real problems started when Joel got a job at Microsoft.