Felix was a whole lot nicer than I was when I initially saw your post, rev! I had put together a pithy reply taking both you and your partner to task when my computer decided to take a data dump!!!!
Your partner totally blew it...as Felix indicated and as you thought, IA cannot occur until the ball is contacted for serve. If there is a problem on the court when checking the line-ups, we fix it (if we can) and play. The
only way that there would be a Loss Of Rally assessed to the serving team before the first serve is if the coach submitted an inaccurate line-up and one of the numbers on the line-up sheet isn't on the court AND no one on the bench is wearing it either. In that instance, since there is a non-existent number listed on the line-up sheet, we change both the line-up sheet and the scoresheet followed by assessing a penalty LOR against the serving team for submitting an inaccurate lineup.
However, if the above scenario was not the case and players were simply in the wrong places - put them in the correct order and then we play! Always remember that as the Referee, you have the final authority over everything that transpires during your match. You have the authority to over-rule your partner if it is absolutely necessary (and in this situation, you should have over-ruled him!).
In Situation 2, as Felix indicated, your partner copped out. There is no justification for calling a replay - you didn't have a net on the home team; he evidently didn't have enough information to be able to call a net on the home team himself (which would have given the point to the visitor), plus...the ball landed on the home team's court which should have been a point for the visitor. So, any way you look at it, your partner made a major error and took a point away from the visitor that should have been awarded.
Time to spray a little WD-40 in the rusty cogs of the volleyball computer that resides between the ears. A check-up from the neck-up will avoid such errors in the future.