Hey Scott,
I've dealt with this quite a few times.
The first solution is capture the Keynote or Power Point through the Video input of catalyst. I do this with my Decklink HD card when I'm doing large edge blended screens and don't get anything but a laptop with a presentation.
The second solution is something similar to what Richard pointed out about creating a quicktime file. This is the method I prefer doing because I can put the whole thing on my laptop and create a quicktime movie at whatever size I want so that I don't loose resolution.
The secret is to count frames and create cues that stop the file at each point when the transition stops. Using a Hog 3, I'll build the main cue to Setup as an InFrame on one list. Then I create a second list with Play modes setup as follows:
Cuelist 2
01 Forward
02 link --> 06
03 InFrame 00000
04 Pause
05 Forward
06 link --> 09
07 InFrame 00000
08 InFrame 00300
09 Pause
10 Forward
11 link --> 15
12 InFrame 00000
13 InFrame 00300
14 InFrame 00600
15 Pause
16 Forward
17 link --> 21
18 InFrame 00300
19 InFrame 00600
20 InFrame 00900
21 Pause
As you can see, the inframes I set with 10 second offsets foe example. The link cues I create a wait time of 10 seconds which skips to the next pause.
Then using a MIDI trigger device, I have a remote with two commands, play and back. This way a user can play forward or skip backward for up to three slides (or more if I add them).
Literally, I can create a cuelist for 100 slides like this in less than 5 minutes.
I have never had a situation where it didn't work.