What size is the house? What size is the a/c unit? If you provide the model# from the condensing unit (outside), the size can be determined. Are there return vents in each room on the second floor? If you put your hand on a return vent, can you feel air being drawn in? Where is the air handler - attic? basement?

There will be a 5 to 7 degree difference in temperatures between floors as heat rises to the top floor.

"I thought ducts need to be cleaned only every 4-5 hours"
- I think you meant "years", not hours. And no, as long as the filter is changed regularly (monthly), the ducts should be clean.

If you have a digital thermometer, and open up the air handler (where the a/c coil is located on the inside unit), you can measure the temperature of the air just before the coil, and just after the coil. This is called the "split" temperature, and should be 18 to 20 degrees on a dry day. Having cool air is one thing, getting it to the rooms is another story.

You may also have leaking ducts, either supply or return, especially if they run through the attic. A supply duct leaking will reduce the volume of cool air flow while a leaky return duct in the attic will draw hot attic air into the system.

A 2 year old house should not have these problems.

Ducane is a builders grade unit made by Lennox.

You could always install a window unit in the master bedroom to help cool the room while you figure out what's going on with your central a/c. Curtains/blinds/shades - anything to reduce the radiant heat gain in the bedroom windows will help.