Are these interfaces configured in "autoselect" mode? What happens when you configure them in fixed mode, e.g. 100Mb/full duplex?
Sounds like a good idea. In the future, I will configure them in fixed mode, it won't hurt.
Even though it may have something to do with the autoselect mode, the whole story still has a bad smell =) I mean, the problem persisted even though I several times disconnected the cable, changed the cable, hooked the Soekris to a Dell 5324 Switch (to a port in autoselect mode) and nevertheless the interface did not get out of the stalled state until I did the ifconfig down/up sequence.