Just to correct something:
The SSI tables are not straight-up navy tables, they're based on Doppler studies, and thus considered "more conservative" than the navy tables.
There are a number of versions of the tables out there, all of them are at best approximations, and just because a dive profile puts you one column over in remaining nitrogen time, doesn't mean much at all. Your instructor should know that! I wouldn't worry about it -- if you look into it, the difference will only be a few minutes either way.
Another way to look at it is compare it to using a computer: there are different algorithms used among computers, just like there are different tables. If you and your buddy have different computers, and they indicate a slightly different RNT, does that mean one is defective?
Finally, unless you are descending vertically to a fixed depth that happens to be on the chart, staying there, and then ascending straight up, the chart has a built-in "penalty", and will be more conservative than a computer. That's the main reason I like using a computer -- no silly penalties for normal multi-level diving.
If you are really worried about it, as you should be for instance, if you have some condition that pre-disposes you to DCI, then I recommend buying a computer that allows you to program in an extra safety margin, and use it. The Suunto computers, for instance, use an algorithm based on "micro bubble" research that gets imncreasingly more conservative for multiple repetetive dives on the same day, and you can program them to provide an increased level of conservatism.
To me the most worrisome thing about the experience you describe is the reaction of your instructor -- obviously not very knowledgeable about scuba.