Interesting. I do notice a very faint "pulsing" when I have "Blank Leading Zero" set to "Blank". Perhaps this is due to only running 3 of the expected 6 tubes.
The pulsing disappears (or isn't noticeable) when all 4 tubes are being lit....
Nice work! It looks like its about the smallest case you could use to contain both boards. One small note: It looks like you could use some nylon washers under the mounting nuts. They look uncomfortably close to those surface mount components.