are my replacement windows being installed correctly?

house is 9 yrs old...all 3 second fl windows in back of house leaked water bad during a thunderstorm a few weeks ago..leak is through the window tracks and or bottom where it rests when you close it..cheap builders grade windows,possibly not the best installation also.[we are not the original owners] we are having all 8 windows in back of house replaced [ 1st and 2nd floor ] but ran into problems..i'm not construction oriented so forgive me if i dont word this perfectly---the replacement windows were measured and made already by a reputable company..they came out to replace the windows but found that what they thought was just the stationary part of the old windows that surrounds the parts that move up and down [glass and its frame] was actually part of the wood frame that supports the windows...therefore the new windows wont fit in the opening unless the old windows are removed along with the wooden frame...the company rescheduled for tomorrow..their plan as far as i can tell is to remove the windows and the wood frames and install new wood flush to the window opening so the new windows will fit...they said this situation is unusual and their course of action is appropriate...my wife is very concerned because friends of ours who have constuction experience are saying that the wood frames should stay and the replacement windows need to be remeasured and made smaller....i dont know enough about construction to question the company but dont want an inferior job done just to keep them from having to re-order all of the windows.... -----this might help also--the company said our windows are "hybrid" in that the frames are wood and vinyl,so when they went to tear out the stationary vinyl part the wood behind it that its attached to comes with it...they plan to remove the "window jams" and make new "sub frames" .....any opinions??..