manual P&R need your help

Are there any warnings from Quartus saying why those modules weren't placed in the positions you wanted? Try to search with the name of the component or the location, if there are lots of warnings.

As a side note, except in some extreme rare cases, you don't need to fix the locations of individual components in your designs. If you have specific timing requirements on some signals, then you should specify them as Timequest rules and let the fitter find the best placement for you. It can even be smarter than you in some cases ;)