Q: They're calculated as zero if you press 'calculate', minutes is the only one that remains blank. So yeah, I'd guess it's the minutes.
A: Yeah, there's no easy way to calculate minutes. Even 2K12 ignores the total minutes it calculates in the box score (which is incorrect because it doesn't take seconds into account so the end result isn't TMINS=5*4*QuarterLength, as it should be, but something close to that. In any case, the minutes you should enter isn't 5*4*QuarterLength, but rather AmountOfQuarters*QuarterLength, or AmountOfQuarters*QuarterLength+AmountOfOvertimes*OvertimeLength to be exact (not *5 in any case; so for the NBA it would be 48 instead of 240). Also, I should note that the tool doesn't handle games that ended in draw, if any basketball leagues have that rule. I've only coded it to handle cases where one of the teams has won.
Q: Add Players doesn't work.
A: Did you save the database IMMEDIATELLY after adding them? I should have the tool do that, it's not obvious that changes could be lost if you don't save immediatelly. -sigh- I've just been doing so much development these days that I don't think of doing even the most obvious things. I'm sorry for the time you lost, and once again thanks for helping me debug NST.
EDIT: Yeah, for some reason it's broken in 0.10.5. I'll fix it and make sure the database saves right after adding the players.
Q: Are players handled by name?
No, Players are by ID, players with the exact same characteristics shouldn't conflict in any of the tool's features.
And I think I know a way to be able to allow the users to rename teams without going through too many changes in the code. I'll just keep the current Name field as is and let the
code work off of that, but I'll add a "Display Name" field in the Teams database table, so that it ignores the name in the tool's controls and shows you the display name instead. So current code shouldn't break at all, and you'll be able to rename a team freely. It'll take very few lines of code to implement something like this.
Adding and removing teams completely however needs more work.
EDIT: Scratch that, I just thought of a way to be able to add and remove teams with not much additional work. Also, teams will be able to "return" to the league, and have their previous stats intact. For example, a team will be able to have played in Season 2 and 3, but not in Season 4, and then be back in 5 and still have its stats from 2 and 3.
On a final note, I'm really sorry for your frustration and all the problems you've encountered. I have to say I appreciate your trying to use the tool in a real-life scenario, which gives me much needed feedback on what I've done right and what wrong, as well as letting me know of any bugs. The tool is in beta so it's not really prime and ready for everyday use, but I hope that you'll stick through to the end, and hopefully with all your feedback the end result will be a lot better than I originally planned. Thanks again.
P.S. Not to play devil's advocate, but the tool has a big "BETA" in its title, so you shouldn't spend half an hour on a single feature without testing it for a bit to know that it works as you expect. So next time, before adding 1000 players altogether, try adding 2-3 at first, and seeing if it works properly. That way you won't have wasted half an hour.

Again, I know it's not your fault that the tool doesn't work as you expect it to, but while in beta, development is still being made, decisions change and bugs may come up at any time. I appreciate your help in debugging, but I don't want you to get all too frustrated by planning on using a feature for so long only to find out it didn't work. Test it with a small sample first, always.
