If ChemSkill is not running well on XP here are 2 possible fixes.

FIX NUMBER ONE:
This is a possible fix for the e HW not running on some XP machines. It
comes from a computer tips page dealing with XP and service pack 2.
Several students have used this fix and now the e homework is running
fine. Please get your parents permission before you try changing these
files.

If you get a message that says, this system file is not suitable for
running MS-DOS and Microsoft Windows applications this is what you
need to know.

The installation of Service Pack 2 can cause a file called
"AUTOEXEC.NT" to be corrupted or deleted. This is part of the Windows
16-bit subsystem and usually lives in the system32 folder.
When you get this error it often means that the setup for that program
uses InstallShield which is a 16-bit program. Since the AUTOEXEC.NT
file is missing, it can't run the install program. Not everyone who
installs has this problem, but some have.

THE FIX:
Double click "My Computer" and then your hard drive (probably C drive)
and open the "Windows" folder.
Open "SYSTEM32" folder and see if the "AUTOEXEC.NT" file is in there.
Chances are it isnt. If it is, then it is probably corrupted. Arrow up or hit
"back" to return to the main WINDOWS folder.

Go down to "Repair" and double click. You should find "autoexec.nt" and
"config.nt" in there. Copy these files and then go back to "SYSTEM32"
and paste them there (CRTL + V). It will ask you if you want to replace
the old ones, say "Yes".

That should do it. Now try running that program and it should work fine.

This information is taken from the website
http://worldstart.com/tips/tips.php/1453 , so please look at it for more
information.

ANOTHER POSSIBLE FIX FROM THE AUTHOR OF CHEMSKILL:
The alternate repair is to install CSF on the C-drive and then go to the Chem3000 folder and
right click on the chemskil app file and then click on Properties. Then within Properties click
on the Compatibility tab. Next, click on Compatibility Mode for and choose Windows 98. Click
256 colors. Click 800x640. Click Apply and OK Then try using Chemskil app file to start
Chemskills.

If running on VISTA; try to change the compatibility mode to XP legacy mode.