As of today you have to send the VR3 back to have the firmware (main operating software) upgraded...they are in the midst of changing so that you can do it via internet. Feature upgrades are done by purchasing it and inputting a PIN into the unit (you do not have to return the unit). I fully agree that there are better options. I like the X1...but may sit on purchasing for a year or two just to see how it performs, as it is fairly new to the market. As previous mentioned I would love to see a user servicable battery as well, but that is purely personal preference on my part.
I would think any algorithm would be unforgiving of violations. Not trying to create drama...but what is a minor violation as opposed to a non-minor violation? With a VR3 if you pass the deco stop you will get a warning and a 60 second countdown to return to the stop depth, where it will begin the stop time over again. If you go past the countdown time, it will then give you a "use tables" message which indicates you have now fully violated your deco plan and recalcs for "best solution" to the surface.
The "weirdness" regarding deep stops is the difference between algorithms...I have used the VPM model from V-Planner and have also used the Buhlmann that is standard on the VR3 and have never had an incident with either. I like the VPM model better for a number of reasons, including the fact that it is a bit "smoother" profile than the Buhlmann, which gives you a couple of deep stops....shorter mid-range stops...and then much longer stops at shallow depths, not to mention I find V Planner a great program.