aberkowitz is right in that it would be nice if you could disable that feature in your projector. We have that same feature in projectors at work, and I think it's because if you accidentally turn it off in the middle of a movie or presentation, everyone's going to go "awwwwwwwwwwwwwwwwwwwwww" and make you feel like an idiot.
If you can't disable it in your projector, I bet there's a way to do it in the remote, but I'm not sure how. Perhaps because I don't use any of the power on/off stuff with the remote, I don't have the option to use that "Power" button; it does nothing for me, and although I would like to be able to assign functions to it, I have not found a way (I don't think it shows up as one of the programmable buttons in the "Customize" menu).
There may also be a way to set up your projector's power settings in its setup. If you entered the make and model of the projector in the Logitech software, it should know about the power off sequence for your projector. If it's not implementing it properly, check all the advanced settings for your projector "device" and see if there's something in there that you can change for that aspect. If you "learned" your projector's IR codes from the original remote, the Harmony site may not be able to take advantage of its potential knowledge of the power off sequence (i.e., since you "learned" the codes, it doesn't know what device you are using).
Sorry I can't be much more help than that at the moment. I'd need to look through the site myself. My best suggestion is to call Harmony tech support. They are actually pretty good, and you will be able to talk to a live person on the phone. If you don't get what you want from the first person, ask to talk to "Level 2 Support" or "Tier 2 Support" or something like that. They'll transfer you, and those guys know more than the first level (even though the first level is pretty good).
Good luck!