When loading a saved game with the PC version of Psychonauts, is it normal to be dropped at a different spot in the level than where you actually made the save? It's almost as though the manual save option is working similarly to a checkpoint save, but I only started noticing this after I'd patched to 1.04. I played a couple hours on the 1.00 version before I installed the patch.

Hi Malagris. :)

I don't actually remember this happening, but if it only moved me a short distance I most probably wasn't paying enough attention. If it doesn't move you particularly far then it could simply be that the save game system takes a snapshot of all your collectables/etc, and then when you return it puts you on the closest of a number of pre-set 'spawn' points. I'm guessing generic enemies reappear too if this is the case.

In the first part of the Brain Tumbler experiment, for instance, I saved soon before I ran into the big shiny-eyed teethy monster thing, but when I loaded that saved game it had me right back at the start of the level with all the fragments and such intact.

I also play the game on a PC and the same thing happens in Gloria's Theater.
I saved the game after collecting the very last figment (at the tunnel entrance that leads to the final Boss Battle). When I went to play again, Raz was back at the area just before the elevator that brings him up to the walkway where he meets the Phantom.
I just figured it took me back to an auto-save point. It was a little annoying because I had to fght the Censors again.
On the other hand, when I save my game in "The Milkman Conspiracy", I must be saving it at an auto-save point because I always start off right where I saved the game.
I try not to save in "Waterloo World" (I plow right through to the end). If you save and then quit, when you go back into the game, all of the Cannon Guys and Censors respawn, which sucks.

Just did a little experiment: I hopped up on the hollowed-out log that leads to the entrance to Sasha Nein's secret labs, and grabbed the marker that was there. Saved the game, then immediately loaded it. When I loaded, I had been moved off the log and onto the path leading from the main campground to that area, but the marker on the log was gone. Is this normal?

On my PC, there are no visible markers (I'm assuming you mean gave-save checkpoints like they have in the latest Tomb Raider games).
On my PC I can save anywhere at any point. I may not restrart exactly where I saved but it's in the general area (though in Gloria's Theater it's not close enough).
When you go back into a game, you'll notice that there are 5 gamesaves to choose from. There is also, at the very top of the list of gamesaves, the most recent Auto-save point. I'm assuming these are the unseen autosave check-points in the game.

My experience is that it puts you at your last checkpoint (where you'd come out after reaching a diff area) and keeps track of whatever you picked up, health, scavenger hunt items, brains, etc.