To see if it helps avoid the infrequent situations where PC104 interrupts cease to be serviced, I changed the second emerald board on the low DSM to use IRQ4:

ddn
set_emerald -e /dev/emerald1 0x140 4
/etc/init.d/emerald start
dup

After that, here's the current configuration. Since the config is saved in the EEPROM on the emerald, it should come up in this state after a reboot:

root@low root# set_emerald /dev/emerald0
current port config:
port 0x100 irq 3
port 0x108 irq 3
port 0x110 irq 3
port 0x118 irq 3
port 0x120 irq 3
port 0x128 irq 3
port 0x130 irq 3
port 0x138 irq 3
root@low root# set_emerald /dev/emerald1
current port config:
port 0x140 irq 4
port 0x148 irq 4
port 0x150 irq 4
port 0x158 irq 4
port 0x160 irq 4
port 0x168 irq 4
port 0x170 irq 4
port 0x178 irq 4

root@low root# cat /proc/tty/driver/serial
serinfo:1.0 driver revision:
0: uart:XScale mmio:0x40100000 irq:38 tx:3573 rx:0 RTS|DTR
1: uart:XScale mmio:0x40200000 irq:37 tx:20 rx:22438852 RTS|CTS|DTR
2: uart:XScale mmio:0x40700000 irq:36 tx:0 rx:2926614 RTS|DTR
3: uart:16550A mmio:0x14300010 irq:116 tx:5235 rx:11378936 fe:19 RTS|DTR
4: uart:16550A mmio:0x14300000 irq:115 tx:27 rx:20225583 RTS|CTS|DTR
5: uart:ST16654 port:F1000100 irq:3 tx:0 rx:0
6: uart:ST16654 port:F1000108 irq:3 tx:0 rx:0
7: uart:ST16654 port:F1000110 irq:3 tx:0 rx:80133446 fe:11 RTS|CTS|DTR
8: uart:ST16654 port:F1000118 irq:3 tx:0 rx:411388 RTS|CTS|DTR
9: uart:ST16654 port:F1000120 irq:3 tx:15 rx:22437904 RTS|CTS|DTR
10: uart:ST16654 port:F1000128 irq:3 tx:0 rx:2947936 RTS|DTR
11: uart:ST16654 port:F1000130 irq:3 tx:0 rx:427094 RTS|CTS|DTR
12: uart:ST16654 port:F1000138 irq:3 tx:15 rx:19230482 fe:1 RTS|CTS|DTR
13: uart:ST16654 port:F1000140 irq:4 tx:0 rx:2945680 RTS|DTR
14: uart:ST16654 port:F1000148 irq:4 tx:0 rx:80119263 fe:17 RTS|CTS|DTR
15: uart:ST16654 port:F1000150 irq:4 tx:0 rx:410093 RTS|DTR
16: uart:ST16654 port:F1000158 irq:4 tx:27 rx:20204969 fe:11 RTS|CTS|DTR|DSR|CD|RI
17: uart:ST16654 port:F1000160 irq:4 tx:0 rx:0
18: uart:ST16654 port:F1000168 irq:4 tx:0 rx:2917645 RTS|DTR
19: uart:ST16654 port:F1000170 irq:4 tx:15 rx:19234163 fe:1 RTS|CTS|DTR
20: uart:ST16654 port:F1000178 irq:4 tx:0 rx:2491823 RTS|CTS|DTR

root@low root# irqs
Counting interrupts over 5 seconds ...

IRQ      Interrupt Type            Total Int  Int/sec   
------------------------------------------------------
3:       ISA serial:               742        148.4     
4:       ISA serial:               819        163.8     
24:      GPIO-l eth0:              58         11.6      
25:      GPIO-l GPIO1-PC104:       1412       282.4     
36:      SC serial:                15         3         
37:      SC serial:                102        20.4      
42:      SC ost0:                  509        101.8     
114:     GPIO isp116x-hcd:usb1:    92         18.4      
115:     GPIO serial:              227        45.4      
116:     GPIO serial:              100        20        
120:     GPIO pata_pcmcia:         8          1.6