Can you meas VSYS and VCRG it shouldn't drop under 3v3. Edit:Are you using USB or external PSU for VIN
I need to check that 3v3 from my vidor. Currently using zedboard for tinkering.Is that dropping 3v3 seen only when using external crystal?
What I see is charging chip that needs to be configured by SW to get right charging and USB current limit. Not sure will arduino do this at startup.One way is to use Lion battery for that J12 connection. That will bypass current limit made by USB power/charging controller