This problem has been duplicated on Redhat 9, Mandrake 9.1, and Mandrake 9.2, so I do not believe that it is distribution dependent. Currently, I am running MDK9.2 with the stock kernel (moving to 2.6 once I get it installed properly, but thats another question).

I have a SOYO KT400, and I have disabled ACPI in order to get the onboard network on this board to work correctly. For internet, I use a Draytek router/ADSL.

The same machine is tripple-boot to Win2K and Win98, both of which show none of these problems.

Symptoms:
GAIM takes forever to log on - just simply sits and waits, and eventually logs in.
Some websites, especially the LinuxQuestions.org forums, sit and wait for a few minutes; Galeon simply says 'Transferring data from site'; and then once it appears to time out, it very quickly loads the site.
OpenOffice 1.0 and 1.0.1, when opened for the first time on a boot, nothing happens for a similar timeout period, and then it begins to go to the disk and load.
FileRoller (Gnome), when opening the 2.6.0-test9 kernel source, appears to sit and wait for some time, then accessing the disk and doing what it should do. The same applies to uncompressing the file to /usr/src. (using the tar command line while in Gnome does not have this problem, so that leads me to think that its a problem with my Gnome config)
I cannot search from Excite.com (the site itself and webmail works fine under Mozilla and Galeon), as it waits forever to load the search page, and I cannot find logitech.com

The actual bandwidth speed is fast, so that leads me to think that it is a timeout issue rather than a slow network connection or driver problem. It could also be a matter of the protocol ordering (a similar problem that older versions of Windows NT would have), but I cant find where it is listed. Still, that would not explain the GUI problems. I have not yet installed the NVidia display drivers this reinstall, but I had done so in the last install, and while making the windows faster, it didnt solve the loading problems.

There seems to be a lot of time just wasted when trying to load the programs where it does not search to the disk immediately.

In Windows, some programs and games would run similarly when waiting to check all the devices (A Samsung DVD drive, a noname 36x CD drive, and a SCSI Yamaha4x2x6 CD-writer [the sole purpose of my Adaptec-2930 SCSI card], and an IBM Deskstar 120GXP on the onboard RAID), so perhaps my problem is something similar.