Could you please provide the screen number you mean as there are two check reconcilation processes in Dynamics - one in Cash Manager and one in AP. I can't see the one in AP so I'm not sure what that screen looks like but I'm assuming it's a grid area? Or are you referring to fields outlined in green?
If it is the latter, then one place to check is the user maintenance screen (95.260) where you can define colors for required fields for each user. I changed my User ID's required field color from red (the default) to green - just for grins - and found that borders on required fields did indeed turn green.
There is a color control in customization manager called "forecolor" but I can't quite figure out what that does. However, it might be worth checking whether there is a "self" level customization (custom2.sequence = 500 and screenid = '0306000' (or '2021000'). You could just export customizations on the screen and scan for the 500 sequence level or the word "color".
I'm not sure if any colors or shading inherit from the Windows default themes controllable at the Windows level in Control panel/display but that would be another place to poke around.
Hope this helps.
Gail J-N