FYI, I also ran into EPS files not being saved with a specified bleed, but in my case the added code "as file type" made no difference.
As firewire ended up doing, I disabled the Custom Bleeds XTension and then my old code worked fine:
[code:1:10caaad299] tell application "QuarkXPress"
set theBleed to 15 as point units
with timeout of 600 seconds
save page 1 of document 1 in file EPSfilepath EPS format Mac color EPS data binary EPS scale 100 bleed theBleed OPI include images
end timeout
end tell
[/code:1:10caaad299]