The application note is market 12/97, so besides Win XP, NT, ME and 2000 not letting you have direct hardware access (and messing the timings of you programmer) new parallel ports work with 3.3V.

The circuit in the AN is assuming a VCC o 5V, since they are using TTL devices (or advanced CMOS with compatible TTL logic levels, whatever... I only do electronics today as a hobby, I almost forgot the details from the classic logic families).

So be prepared to:
- have a DOS boot disk to use your programmer
- mess with the circuit so part of it will work with 3.3V and part with 5V.

I did this with an EPROM programmer... a zener to lower the VCC to the counters, 5V to the EPROM... a mess, but worked :-)