Manually applying -dVER2 is not enough. It should be, though.
Just adding a {$IFDEF VER3} isn't either, it seems

Btw: the missing windows functions should be covered in KOL_ANSI.inc and KOL_UNICODE.inc.
That's why I suspected a change in the parsing. This used to work with trunk until VERY recently.
That's very strange. The only place I can find MakeIntAtomA in both FPC 2.6.4 and trunk is in jwawinbase.pas. And TFNFontEnumProcA isn't to be found in either. I checked all *.pas;*.pp;*.inc files with ScanFS from Saleen. A.F.A.I.K. that should cover the whole source of FPC itself. Both are also not defined in KOL itself. So I find it strange it would work in an older version of FPC.
The only way this would have worked is if the whole KOL_ANSI.inc wasn't included in KOL. But since the source hasn't changed since feb 28th and KOL_ANSI.inc is always included for IFDEF WIN this would be very strange.
In what version did it work? (Did is work in 2.6.4 for you) If so, maybe you can check where the MakeIntAtomA is taken from. You could check why it's valid in that version.
I did notice the following note of yours in the KOLDEF.INC
FPC version 2.1.1 is very compatible with Delphi and kol now.
You can simply use the $(DELPHI)\source\rtl\win\*.pas files from Delphi 4/5 instead of the prepared files that were needed for FPC1.X
And yes... if you use the Windows.pas from Delphi 4/5 it will probably work. That one
does have MakeIntAtomA declared in it. So my guess would be that you had the Delphi Windows.pas in your FPC source somewhere.