Hmmm, it helps if you actually measure the cruiser in question instead of assuming that its 3" long. Doh!
Please disregard silly original post...
OK, lets try this again. Imperial cruiser is 3.5" long and 3km long in the chart (link at bottom of page).
1" = .86 km = 1:33858
1mm = 33858mm (33.86 meters)
1cm = 338580mm (or 338.6 meters)
1/16" = 1.6mm =54.176mm (or 54.176 meters)
Imperial launch bay ports are 2mm x 3mm, so are 68 x 100 meters.
Moving on to the "new" scale...
In the FFG Rogue Trader books an Imperial cruiser is roughly 5km long.
1" = 1.4285714 km = 1:56243
.70" = 1km
1mm = 56243mm (56.243 meters)
1cm = 562430mm (or 562.43 meters)
1/16" = 1.6mm =89989mm (or 90 meters)
In this scale Imperial launch bay ports are 2mm x 3mm, so are 112 x 170 meters
http://the-first-magelord.deviantart.com/art/Battlefleet-Gothic-Scale-Chart-82219217