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Do you mean a 2003 Matrix XRS?
Does turning off the off A/C after some time always make it work again?
Sounds like the system is freezing up on you, like a home A/C system. Generally this is due to a low refrigerant charge or moisture in the lines. Can also be caused by a faulty thermistor and expansion valve. A bad relay can also be the cause - but should also kick the A/C light off as well. Low refrigerant, wrong oil additives in the refrigerant, bad seals, etc. can all cause a drop and line pressure - the compressor has a safety feature that causes it to cut out in the event of low refrigerant. Also the magnetic clutch mechanism could be intermittent - if that cuts off, the pulley will flywheel and not turn the compressor.
Have you verified that the A/C compressor is still turning (look at the pulley) when the A/C quits?
Notice that there are any frost on the piping under the hood?
Assuming you've already cleaned/replaced the cabin air filter?
Verified that the condensation drain is functioning properly and not clogged (water should be running from the bottom of the car when the A/C is on)?
Have you verified refrigerant level from the sight glass on the receiver on the system (should be right by the radiator, look for the long aluminum tube with metal pipes coming from it, little glass window is on the top)? If you see some bubbles as the A/C is running - level is fine. If you see no bubbles (completely empty or over filled) or lots of bubbles (partially filled) - then you know that the charge is not correct. Gauges (high side and low side) are the correct way to check the charge, but the sight glass will confirm or deny the levels are valid.
Given the number of potential culprits - both electronic and mechanical. I'd take it to another shop and have them verify the A/C charge. Some places will completely evacuate the system and recharge it - they should be able to tell you if they found moisture in the line or not. Visual inspections can catch most of the problems - like frost on the line, clogged drain, intermittent mag clutch operation.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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