All my synths since late December last year have been composed of 3872 x 2592 images and I have no problems with it. Sometimes, yes, there are errors with an upload, but I don't believe they have anything to do with the size of the images because I would occasionally have them before I got my current camera.
What Photosynth does is divide each of your photos into several resolutions and divide each of those resolutions into a series of jpg tiles. I don't know what quality setting it's saving those jpg tiles at, but if compression is taking place, it would be here. Before these collections of tiles are uploaded to the site, they are zipped up (.dzi = deep zoom image; dziz = deep zoom image zip). You can test this the next time you're making a synth by typing %temp%/photosynther into Windows Explorer and copying (not moving) one of your dziz files out of the images folder. Add .zip to the end of the filename and you should be able to peek inside.