Lorgy: I think it's difficult to see things from each's perspective as you were at one end of the spectrum and I (and others) were at the other end. I'm a Manager over at reRroRemakes.com and judged most of their competitions, some of which were huge (with £thousands in prizes), and this issue never came up once as we ensured it didn't. Multiple entries of the same game were not allowed.
In no way do I hold you responsible or accountable for inaccuracies/problems in judging, but it's better to prevent a problem, than attempt to cure one after the fact.
Preventing the same game being entered in two formats would remove this problem completely - irrelevent to the number of judges there were (and remember, you had difficulty getting reliable judges in the first place IIRC - it took way too long to get the results). What makes you think that there will be 5 or six people wanting to judge a comp like this nowadays? There seem to be far fewer people here now than ever before (for various reasons)
However, even refusing the same entry on separate formats causes issues - the coder would have to think tactically and decide which format his/her game would have the most chance of winning on?
All: It might be a good idea now to put out feelers for who would like to judge (and which formats they can judge on), who might participate. If no potential judge's own say, a Caanoo, then that format can be removed from the competition immediately.
Timescale-wise, anything under two months is too short, anything over three months is too long. Start date, I'd say Jan 1st - New Year, New game comp.
Anyway, I've said my piece(s) - I'll leave it upto others to voice their opinions now