Okay, so I've downloaded Gabriel Knight 2 from GOG and am playing it with dosbox on a laptop with Windows Vista. My problem is that in chapter three, during the puzzle where you have to use the cuckoo clock in the hunting lodge, the game doesn't give me enough time to go back to the front room while Xaver is distracted.
I feel like this must be a timing bug because I know what I'm supposed to do, the game simply doesn't give me enough time to do it, and Gabe moves very slowly while going from room to room. Is there any way to fix this?

Maybe try a different graphic mode with the graphic mode setup tool (game start menu folder) to see if that corrects Gabriel's pace.
And tick the 'Run as Admin' checkbox on the game shortcut. Probably won't help much with this particular issue but you never know.
Edit:
I just thought of something else. After an animation starts, you can click to skip that animation. Have you tried that ? Clicking as soon as the animation of Gabe walking across the room with the fireplace starts should place you instantly next to Xavier.
Edit 2:
Edit2: Hang on. You plant the clock, you go back to Xavier, THEN the clock sets off and Xavier goes to check out the noise. You're not supposed to go back to the front desk while he's distracted, you're supposed to be right next to him at the front desk when he first gets distracted.

Try lowering your cycles (Ctrl+F11)

Changing the cycles doesn't seem to do anything but crash the game if I set it too low. I went to see what I had the cycles set on (4000) and tried putting it on auto but that didn't change anything, and neither did setting them higher.
Changing the graphics mode causes my saved games to disappear, and anyway the mode it was already on (Overlay) seems to work best, so I don't think that would help any. Checking 'run as admin' also gets rid of my saved files, and unchecking it makes them come back.
I have tried skipping animations, but that doesn't seem to give me any extra time. Namur, you're right, though, you're supposed to get to the front room before Xavier goes to check the noise, but I only have a few seconds before the fireplace animation shows up where Xavier walks back and forth between the rooms. It actually doesn't seem to matter how fast I am, as when I click on the exit from the fireplace room into the front room I get the same animation of Gabriel sitting by the fire while Xavier walks to the hallway and then back. After the animation occurs the game seems to freeze up and won't let me leave at all.
I'm wondering if starting from an earlier save will fix the problem, but I haven't tried that as my earliest saved game is from Chapter 2.

I don't think not having 'Run as Admin' ticked is the issue in this case. However, if you wish to keep the run as Admin ticked and get the game to find your saves just copy them over from
C:\users\<your_username>\AppData\Local\Virtual Store\Program Files\gog.com\Gabriel Knight
to your game folder. Copy, don't cut and paste, that way you'll leave a backup of your current saves in the Virtual Store folder
You need to copy all the GKSG.000, GKSG.001, etc and the GKSG.CAT files.
If you can't get past this issue by starting from an earlier save, or if you don't feel like playing through CH2 again, i can upload a save game right after the cuckoo clock bit. Just let me know if you think it's worth a shot and i'll upload it.

I wonder if the solution posted in this thread [url=]http://www.gog.com/en/forum/gabriel_knight_series/technical_issue_on_day_6/perm=2/#p_b_2[/url] would work on Gabriel Knight 2? I know this second game is fmv but does the dosbox config for the game have a cpu= option you could change?

Use core=normal and 10000 is about the best starting point for cycles for SCI games. any faster and you can start to uncover the timer bugs. Even 10000 is too fast for some of the earlier SCI VGA games. You really should not have to go lower than 7-8000 cycles for any SCI game, and that only if you get the "Unable to initialize your audio hardware" error, which is not an issue with this game.