Hi Karolina
I assume that you are using a Rev-D right? The temporarily drop of supply voltage is caused by a diode.

While you are supplying with P5_9V_Vin there is not diode, but when you connect USB to OpenSDA and it supply power to the system, you have a diode that cause a temporary drops of voltage. If you check schematic od Rev-E or F there is a diode in P5-9V_VIN. Also I have made a test of this and it only occurs in Rev-E schematic.
Hope this information helps you
Have a great day,
Jorge Alcala
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