So to put those answers in to perspective,
Q: Can it actually do 3A at 5V?
A: Well the PSU is rated for 5A, not 3A. So, even if it was a lower amperage at low voltage levels, would it be enough to stop the MiSTer from operating properly?
Q: Is the built-in voltmeter accurate? Have you tried checking the output with a multimeter?
A: It's pretty accurate, I did test it and it's out about 1/10th of a Volt. So not enough to cause any major issues I believe.
Q: Is the output connector center positive?
A: Yes, it is positive. Although the barrel doesn't fit all the way in like the original L.T.E supply. Plugging a negative charge in to your MiSTer DOES fry it.. at least my friend did so and we had to send it back to Terasic for a repair, it had blown a transistor.
The other possible culprit could be the .ini or the SD Card itself. When I sold my other MISTer, I left my preferred SD Card in it by accident. But, I am finding something inconsistent. When I changed the configuration of the ini's, the plain fuzzy screen that displays is shown but with out any differences (No change in OSD appearing, or even vertical hold which seems odd.)
I'll know more by tomorrow, I ordered a new SD Card, and am having the Buyer with my good SD cards send me my lost .ini's this evening. If I still have failure after those updates, I'll return the PSU and look for something recommended.