Bad idea? Powering uC from two separate supplies?
You have very close voltages for your supplies, but connecting them directly to each other could push/pull excessive power to/from your programmer (the MB will likely have a more powerful source, and not be the first component damaged).

One simple way to avoid problems, if your uC is like mine and has a wide supply voltage range (at least down to 2.5V for this purpose) would be to simply attach a switching diode in series with the +Vcc trace from each possible power source; then your uC would simply draw power from the highest-voltage connected power source.

Alternately, you can add a SPDT signal relay to your uC on the power trace. Attach the coil &amp; NO pins to the MB power supply trace, and the NC pin to the programmer power trace. That way any time there's avail. power from the MB, the programmer power supply sees an open circuit, but when MB powers off, the uC won't back-feed power from the programmer to your MB (and probably overllad the programmer's supply).