Probably a bit late, but here are the best fixes I found:
First off, you want to:
*** Change compatibility to Windows XP (SP3)
*** Disable Visual Themes
*** Run as admin
Next you want to:
Download the pharaoh exe files (these are for modifying the resolution - this is what worked for me - I used the lowest res available, so I cannot comment on higher ones)http://www.wsgf.org/dr/cleopatra-queen-nile/en
Or you can try this fix:https://web.archive.org/web/20080721084339/http://www16.brinkster.com/salvage/thief/imagecfg.zip
Extract the .zip and place imagecfg.exe in your game's folder.
Create a batch file. First, open up notepad and paste the following.
if not exist Pharaoh.exe goto end
if exist Pharaoh.exe.bak goto end
copy Pharaoh.exe Pharaoh.exe.bak
imagecfg -u Pharaoh.exe
imagecfg -a 0x1 Pharaoh.exe
Save as a .bat file and place it in your Pharaoh installation folder.
Run the batch file.
This will change the CPU affinity of Pharaoh so it will run on one CPU core."
This fix taken from here:http://pcgamingwiki.com/wiki/Pharaoh