It's really weird but I've confirmed it multiple times on my machine.
When I boot install of slackware it effectively disables my notebook fan.

I didn't believe it, at first I didn't believe it, I enabled an option in my bios to "enabled always on fan when on ac power"

Boot pc with this bios option on, fan kicks out good amount of air.
Boot slackware install, fan dies and kicks out nothing.
Continue with install, get to around about package choice stage an console throws up a thermal critical message, by this point heat can be physically noticed around CPU area and hot smell becomes present. If continue it only gets hotter and smells worse. I shut Dow. Before damage.

If I switch on after shutdown fan is back on and working 100% and machine kicking out really hot air and smell but cools down quickly.
Fan stays on constantly unless I boot slackware install.

Past week or so I've been playing with these installs and running fedora constantly with no problems with heating at all
Saybayon
Debian
Vector (vers 6)
Fedora 13
Mepis 8.5

My notebook is HP nx6110 1.7ghz core duo. Low rpm hdd. Fan and sink in great condition.

This is a major issue surely?

Not very surprising, the Slackware install environment is very simplistic, it doesn't include anything as advanced as software fan control. The issue is most likely due to the vanilla kernel shipped with Slackware, rather than the tweaked and modified builds other distros ship with.

Getting fan control working once Slackware is installed isn't a problem, but off the top of my head, I can't think of an easy way to get it included in your install environment. Perhaps somebody else has a different take on this issue?

Neither Slackware 13.0 nor 13.1 default installations controlled fans on my desktop; they installed the lm-sensors package but it had to be configured and the boot scripts modified to start it before there was any fan control.

Using one of the other distros, best the one that has the closest kernel version to the Slackware 13.? you want to install, you sould be able to find the fan control file(s) by
It/they might be in the /sys/devices/platform/<chip ID>/ directory. cat the files to see what values the kernel is using for fan control.

Armed with that information you _may_ (this is a long shot) be able to workaround the problem at the step where you normally have to type setup by using echo to write the normal value to the /sys/devices/platform/<chip ID>/fan*_input file(s).

If that does not work, it may be useful to know if the problem happens if you get to the step where you normally have to type setup and do nothing. Will the problem happen then or is it being created later in the installation?