I have seen misalignments in all versions, not just in 0.9.0. As for the problem occuring only with large projects, I don't have this impression. I have had misalignments with 30 images and have had perfect alignments with 700 photos in the first run. I think this might simply be due to more photos meaning more possibilities where things can go wrong (e.g. higher chances of some photos having poor texture).
Regarding the time you need to re-align all photos: most of the processing time in the alignment is used for (1) finding points, (2) selecting image pairs if you have chosen "pair preseletion" and (3) matching points. For large numbers of images, pair preseletion already reduces processing time a lot. Also, after you have run photo alignment once, PhotoScan remembers the matched points. So if you then select all or some images and then right-click "re-align photos", PhotoScan will use the matched points and recalculate only the photo alignment itself (i.e. perform the actual bundle adjustment). This takes only a fraction of the time you would need for the complete alignment. On the other hand, using the menu item to align photos will start the entire process.
Also, if you de-group the cameras under "camera calibration" (i.e., choose "separate"), this can help to improve alignment, in particular if anything moves within your camera/lens system (e.g. focussing, optical image stabilisation).
As a final note, right-clicking on one image and choosing to re-align that one image will cause PhotoScan to re-align that one image to the existing project AND to re-optimize (but I believe not truly re-align) the bundle adjustment and camera calibration for the entire project (you can see this when comparing refined camera calibration parameters before/after doing this). This can sometimes be helpful when you see minor flaws in your final model.