Third party health monitor software has to be configured for your mobo unless a canned config is supplied with the software. Some PSUs still have a -12V line and/or a -5V line (my Zippy has both). the -5 is no longer required by the recent ATX specs and the -12 may be gone shortly. Look on the health page of your BIOS setup to see if it is reading a -12 line. If it is, then the software is reading the wrong port address for your mobo for the 12 line(s) value(s).
. Believe me, if your +12 was actually near -12, then your system would never boot.
IAC, a meter reading should be more accurate assuming a halfway decent meter.
.bh.