In that case I have no idea what is causing you problems. The game was designed for that type of screen. It's a kind of relic too. 
The graphics of the original were not that good but it was certainly playable.
The two mods BGT and Tutu do improve clarity which is just one of the reasons why they are so popular.
Are you playing full screen or windowed mode?
First thing to try
1) Right click config.exe.
2) Select properties.
3) Select the compatibility tab.
4) Select the windows XP service pack 2 option.
If that solves things fine. If not:
Go into the save game menu, there is a box called graphics.
Select it.
It is here that you can select full screen or windowed mode.
There are then a few options to select.
Try selecting software standard BLT. it says "Enable this option if graphic anomalies appear in the game." My game doesn't have any anomalies, but it sounds as if yours does. 
Please let me know if this solves things. Hope that helps. 