Humming problem my brand new mackie once power on gives humming sound and then for awhile it makes a thunderstorm like sound without signal and master vol. completely off.

Check cables first, then make sure everything is plugged into the same power ground. Hum is always caused by bad grounds or bad cables. Otherwise you have an internal component failure and without more information Im not sure which one it could be.

Almost certainly the amp has failed, as per usual with these, you need to take it to the repair shop and see if it's worth fixing it then sell it once working or for spares if not. Sadly whilst Mackie make some really good kit their powered speakers are not amongst the most reliable

This sounds like a ground loop.
Make sure that everything in your signal chain (mixer and anything that plugs into the mixer, and the L1®) are all plugged into the same power source (power bar).
More tips here:
Ground Loop Bose L1 Encyclopedia FAQ Wiki

This type of active speaker by Mackie has a issue with operational amplifier ic's inside, they are just those little black things with 8-pin soldered to the pcb, you may have some of them damaged, because of the erratic operation of the units, let me know if i can help more.

You say the clip light is always on, as the only clip lights on this mixer are on the effects channel and the master output and you do not say which is on there are a number of possibilities. You may have the effects turned up too far as this should not be showing, just maybe blinking, turn them down on efx2 on all strips as well as on the effects processor and see if this helps. If it does you may be able to find where the hum is coming from by gradually increasing each until you find it.

If you are getting the clip on the main mix master and you are not being deafened and the humming sound is coming from the speakers not the mixer you may have a subsonic signal getting into the mixer. Disconnect all inputs and if this cures it go through until you find where it is getting in and sort that.

If the humming is coming from the mixer it is possible that the smoothing caps on the PSU are dying, you do not say if you are getting normal sound as well as the humming from the mixer.

When asking for help please try to give as much information as possible

Make sure ALL of the interconnected equipment is powered from the SAME receptacle to avoid ground loops due to the safety ground. DO NOT Use two wire power or use ground lifting plug adapters. Make sure you use balanced lines, either XLR or TRS cables. Do NOT use TS cables.

What cables are you using? I have found brand new XLR cables that were mis-wired causing hum.
Check that the signal wires connect to pins 2 and 3 in the connectorss and that the shield is tied to pin 1.

Find images of the pin positions here:

http://www.google.com/images?hl=en&expIds=17259,27740,27760,27796,27824,27867&sugexp=leprodsca4&xhr=t&q=xlr+pins&cp=7&wrapid=tljp1291152977062014&um=1&ie=UTF-8&source=univ&ei=V271TMPdLoj2tgOK2PG7Cw&sa=X&oi=image_result_group&ct=title&resnum=3&sqi=2&ved=0CDgQsAQwAg&biw=1233&bih=570

Make sure the speakers are powered from the SAME receptacle as your mixer !!!!!

If you are using 1/4 inch connections they MUST be TRS type using BALANCED lines to avoid hum.

Try hooking your mixer up to your Mackies without the laptop. Does the hum go away? Try hooking your laptop output up to the Mackies without the mixer. Does the hum go away? Make sure that all your power cables run from the same outlet and have the ground or third pin intact on the plug. Also make sure that you are using shielded cables for any connection that carries an audio signal. This includes the cables going to your Mackies as they are powered amplified monitors. Make sure that the cables to your Mackies are balanced and haven't been altered to unbalanced. You will need to use unbalanced cables from your laptop unfortunately but try to find ones with a shield and three conductors ( right and left signals and a common or ground) that have a separate shield from the common. The shield should only be connected to common at the output of the device where the signal starts. A better explanation is at these links:http://www.epanorama.net/documents/groundloop/ also http://www.epanorama.net/documents/groundloop/cable_shielding.html

If the hum is observable in headphones, then it is likely a power supply problem, usually a dried out electrolytic filter capacitor.

If you disconnect the signal leads and the hum is away, it's probably a groundloop problem, or your equipment is generating the hum.
If it does not go away, the amps are defective