OK I found it, with Google's help...
Apparently I need to add 'vlan and ...' to my filter expression when VLANs are used. Without filter expression, tcpdump and libpcap just output everything, but as soon as filters are specified, the vlan tagging needs to be specified.
See here
Blog Stéphane Bortzmeyer: Un exemple de panne amusante de tcpdump
Hope it is useful to others as well.