I just tried a slot in a very recent testing version (Oct. 29). This is what it outputs for a 1x3mm slot (excerpt with relevant commands) - I think it may be fixed. Anyone who knows more about Excellon format want to comment?
G90
G05
T1C1.000
X144.018Y-83.836G85X144.018Y-85.836
G85 (buried in the last line, if you missed it) is the "slot" command. There are a couple other ways that can do it as well - I believe what KiCad used to do is to specify that the drill bit be dragged down the length of the slot (quite bad for the type of bit used).
From the way old versions used to work (not just the slots), I got the impression that the KiCad people thought Excellon was just a funny vector graphics format...
In the test I just did, I did get a 2nd excellon file. (.drl) for kicad.
I have no idea of what it should look like but here it is.
M48
;DRILL file {Pcbnew (2013-09-28 BZR 4356)-product} date 5/11/2013 11:45:09 AM
;FORMAT={-:-/ absolute / inch / decimal}
FMAT,2
INCH,TZ
T1C0.055
%
G90
G05
M72
T1
X2.4791Y-3.8775G85X2.6209Y-3.8775
G05
T0
M30