My house is 6 years old. The master bedroom has two floor vents. One makes a clunking noise like someone is knocking on the duct about every 5 minutes. The other does not. The only thing I could think of is that the vent was not securely attached to the floor; so I put some nails in it. That seems to have made it louder. From the basement there isn't anything apparent. In the quiet of 2am, there are various noises coming from all over the duct system, but this one particular vent seems to be worst.
No particular noise is coming from the furnace.
You didn't elaborate on when the noises are.... just every 5 minutes. Is this only when the furnace is running? When the furnace fan first comes on, after it's been on awhile, when the furnace has quit buring and the fan is still running? Only during the night or all times of the day?
Is all of the ductwork accessible? IE: Single story house with unfinished basement.
Most times noises in the ductwork come from three sources. Expansion and contraction as it heats up and cools down OR flexing noises that are heard when someone walks on a certain spot in the floor OR flexing of the ductwork when the blower first comes on or shuts off.
The expansion and contraction noises are usually from the ductwork rubbing against something while it expands and contracts in it's length, this rubbing can also be in "spurts or jumps" if what it is rubbing on holds it for a small amount of time then lets it slip. These noises are usually only heard when the furnace is running and then are usually more pronounced during warm up and cool down of the ductwork.
Flexing noises from the ductwork only happening when someone walks on the floor above it are usually due to it being in direct contact with part of the floor framing that is flexing.
Flexing noises from the ductwork when the blower first comes on or shuts off is caused by the ductwork expanding in it's height and width measurements..... it's like blowing up a balloon. This noise usually sounds more like a popping noise.
Once you figure out just when it's making it, it's easier to find where the noise is coming from.
The rubbing expansion noises can be cured by placing something between the ductwork and whatever it's rubbing on to make it slide easily and without sticking. It could be rubbing on wood, wires, water pipes, other metal supports or items.
The noises coming from walking over the ductwork are a little harder to cure, but basically require the same isolation from whatever it's rubbing up against. Sometimes it's just a matter of loosing up a hanger the thickness of a couple sheets of paper.
The popping noise flexing is fixable too. The fix for this can only be figured out once you figure out what piece is actually making the noise. Sometimes simply dimpling the longer dimension with a blow from a hammer will stop it. Sometimes you have to screw a stiffener of some form to the metal.
You're going to have to play investigator to figure out the what and why so you can come up with the how.