Thanks a lot for your answer, very instructive !
Like i answered in my previous answer, im quite positive now that the main culprit was these loose banana connectors (the same used by old Serge modular synths, but these were cheap ones).
After replacing them, everything seems to work nicely.
Still, I reflowed some joints, and will add 10nF +100uF decoupling caps near arduino and the RTCl. It can never hurt i guess.