If you calculate the credit yourself by using the worksheet on the third page of the Schedule M instructions (posted earlier), you'll see the credit is based on 6.2% of your earnings, up to $400. When calculating that earnings figure the worksheet directs you to subtract any amount excluded on Form 2555/2555-EZ. I didn't make this up, it is there in the official IRS guidance. If your tax software is not doing this it is getting the calculation wrong.
If your total income including 2555/2555EZ exceeds $75k single/$150k married then your credit is reduced by 2% of the excess amount. So it does come into the calculation of the credit, but it can only hurt you!
I can say when I did my taxes using H&R Block the Form 2555 amount was subtracted from my earnings, as the IRS directs. Perhaps other software is not following the instructions.