I am powering a Arduino Uno R3 with 12v using the barrel jack. When measuring with a multimeter, instead of reading 5v from the 5v pins (or any other digital pin for the matter) I see 3.3v; and from the 3.3v pins I read about 2.6 .
If I power the board via USB from my laptop, it all works fine. I'm guessing that this indicates an issue with the 5v regulator; I'd like to know if there can be anything done besides using an external voltage regulator and connecting it to the USB power lines.
Is anything connected to the Uno?
There is a piezo disk and a resistor in parralel conected to A0 and ground, and a wire from pin 7 to a 3d printer board to trigger the endstop pin.
Disconnect all the loads and re-check the 5V, with the barrel jack powered. What test points are you using to make your voltage measurement?
Tried it; no difference in behavior whatsoever
I am measuring from the built-in 5v and 3.3v pins, and also pin 5 set to HIGH for troubleshooting purposes
Have a close look at the 5V regulator chip. It may be a 3.3V regulator for whatever reason.
To where?
and... did you measure the 12V?
The USB jack's case makes a handy GND point.
A switch mode step down module will greatly outperform the on board regulator, anyway... so maybe you should consider it.
To where?
to the board's ground pins
ok, just being sure... I've actually seen an MSEE try to measure a battery with only one test lead. 
A switch mode step down module will greatly outperform the on board regulator, anyway... so maybe you should consider it.
Probabily gonna do that, as for my usecase it doesn't matter if the board is powered via usb or the barrel jack
Are you using 12V for anything else? USB power is usually a better choice.
I guess the battery in your multimeter is flat.
A cheap DMM could do that without giving you a warning.
As others said, 12volt on the DC socket is in the danger zone, and you can't power much from the Uno at that voltage without overheating the 5volt regulator. A 5volt cellphone charger, connected to the USB socket, is a much better power source. That will bypass the 5volt regulator.
Leo..
Are you using 12V for anything else? USB power is usually a better choice.
It also powers the heated bed on a 3d printer
I'm using a standard 350w 12v power supply
If you have 12V available, you might as well use it with a step down. It would save you a space on the AC power strip for the USB charger.
12V is in the range where a relatively small load on the Arduino 5V or pins can produce a lot of heat in the on board regulator. Better to go with a switching supply.
Quick way to test, measure the 12V supply since it presumably is actually 12V.
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