Things are smooth/snappy on my ALIX with a snapshot from today, I've not seen this slowness myself. Saving does take about 6-7 seconds but it always has on ALIX.
Using HTTPS to get to the GUI, everything seems happy.
I have a soekris 4801 (and a couple of 4501's, but not enough ram). Works fine with 2.0.1, but every 2.1 snapshot I've tried in the last week or two exhibits the stall problem.
A number of people have mentioned shell commands like 'ls' hanging etc. If you type ^T (ctrl T) during one of these stalls you'll see that the process is waiting on suspfs, which is one of two functions in kern/vfs_vnops.c (both vn_start_write and vn_start_secondary_write call msleep with the same wmesg string. usually the wait message is unique so that there is no confusion which [tm]sleep we're waiting in. I think this is a bug in itself and the msleep in vn_start_secondary_write should be changed to "suspf2" or something similar to differentiate it ).
Anyway, seeing that processes are stalling in either of these functions leads you back to the mount updates being the cause. If you run /etc/rc.conf_mount_ro from a shell, followed by /etc/rc.conf_mount_rw I see a stall on the second command everytime. ^T reports that the mount process is waiting on biowr.
I put some logging into /etc/inc/config.lib.php (where conf_mount_ro and rw function reside) to determine which of the 4 mount updates was stalling (syslog conveniently timestamps the messages) and it's the read only mount update of /. On my system it's a stall of between 107 and 110 seconds.
I can't reproduce the behaviour using the same image under virtualbox.
The CF card in this 4801 is a cheap card with a brand I had not heard of, I'm going to try a sandisk card when I can find it.