For your information, I stumbled over a stupid little mistake on the rev0.4 PCBs yesterday evening.
During the development I used 3 different SD cards and everything worked fine.
Yesterday I tried a newly aquired SD card from a different brand.
As it seems, when inserted during runtime, the voltage drop caused by this new card is enough to cause a brown out error on the mainboard.

Booting with the card already inserted works like a charm.
An additional electrolytics cap between the 3V3 and GND rail on the frontpanel board fixed the issue. I used 100uF but probably 47uF is enough, I will try it out and let you know.
So if you experience problems with hotplugging your SD card, you may have to airwire an additional cap between 2 pins of the mainboard connector.
Will be fixed in the next batch of PCBs
Comments
the lower pin is GND and the upper pin is 3V3
Are you sure you had the right polarity and the correct pins?
A simple reeboot did not fix it?
The new haven displays are a little bit picky about their cv's.
even a simple reboot of the AVR during programming causes these displays to show scrambled data
:@)
have you tried to read the card on a PC?
4050 IC: sits tight in the socket, no cold solder joints
all pins on the sd card socket on the mainboard attached firmly (should not move if you push them lightly with screwdriver or needle)
the cap has nothing to do with this. without the cap the mainboard stops responding with some cards when you insert them while the synth is running. The "init error" indicates that the synth can't communicate with the card. so either the filesystem is damaged (then it should not work on the PC, too) or a connection came loose.