If you disconnect the pump and replace it with a led and resistor, does the RTC function correctly ?
What I am trying to get at is if your problem is 'electrical noise', power surge etc. when the pump is started.
You said in the OP "Everything works OK when its powered thru the USB", but since then, you've now said that the pump is 12v so "Everything" did not include the pump. That is, if I understand you correctly.
This looks like a specification of your power supply.
Have you also tried powering the Uno through the 5 volt output of your dual volt power supply ? Use the pin marked 5V on the Uno.
Anyway, you can wait until you are able to post a schematic before replying.