DEC 1000A 5.0.0_PATCH system has problems booting after upgrade from 3.1_STABLE

[Paul Mather <paul%gromit.dlib.vt.edu@localhost>]

Recently I posted about needing to upgrade from netbsd-3 now that it  
is end of life.  I decided to upgrade to netbsd-5-0, and, aside from  
some space problems (oddly enough, on /usr, not / as I'd been fearing)  
I managed to sort out, the upgrade was successful... well, largely so.

I have one problem: the system hangs at the console when trying to  
reboot via "shutdown -r".  NetBSD manages to shut down properly.   
Unfortunately, the system does not manage to reboot successfully.  It  
hangs at the console.  This happens both when using my custom kernel  
and a GENERIC kernel.  I even updated the bootblocks from the old ones  
(NetBSD/alpha 1.6K) to the ones in 5.0.0_PATCH, all to no avail.

I never had this problem under netbsd-3.  It has only appeared since  
upgrading.

Here is what I get on the console after shutdown:

=====8<=====
halted CPU 0

halt code = 5
HALT instruction executed
PC = fffffc0000300118

CPU 0 booting

Invalid mode
TU PCI Bus Error :CSR5: fc90a000
waiting for pka0.7.0.2000.0 to start...
waiting for pka0.7.0.2000.0 to start...
waiting for pka0.7.0.2000.0 to start...
waiting for pka0.7.0.2000.0 to start...
waiting for pka0.7.0.2000.0 to start...
(boot dka0.0.0.2000.0 -flags a)
=====>8=====

The system then just seems to hang and never boots off the disk.   
There are no problems booting from power on or from a hard reset.   
This leads me to believe that the shutdown under netbsd-5 is perhaps  
leaving the hardware in an unclean/inconsistent state that prevents a  
clean boot.  (Like I said, this only started happening post-upgrade.)

Here is my system dmesg:

=====8<=====
Copyright (c) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,  
2005,
    2006, 2007, 2008
    The NetBSD Foundation, Inc.  All rights reserved.
Copyright (c) 1982, 1986, 1989, 1991, 1993
    The Regents of the University of California.  All rights reserved.

NetBSD 5.0.0_PATCH (CHUMBY) #0: Wed Jun 17 23:24:13 EDT 2009
        paul%chumby.dlib.vt.edu@localhost:/usr/obj/sys/arch/alpha/compile/CHUMBY
AlphaServer 1000A 5/300, 300MHz, s/n
8192 byte page size, 1 processor.
total memory = 128 MB
(2016 KB reserved for PROM, 126 MB used by NetBSD)
avail memory = 118 MB
timecounter: Timecounters tick every 0.976 msec
mainbus0 (root)
cpu0 at mainbus0: ID 0 (primary), 21164-5
cia0 at mainbus0: DECchip 2117x Core Logic Chipset (ALCOR/ALCOR2),  
pass 3
cia0: extended capabilities: 20<DWEN>
pci0 at cia0 bus 0
pci0: i/o space, memory space enabled, rd/line, rd/mult, wr/inv ok
pceb0 at pci0 dev 7 function 0: Intel 82375EB/SB PCI-EISA Bridge (rev.  
0x05)
ppb0 at pci0 dev 8 function 0: Digital Equipment DC21050 PCI-PCI  
Bridge (rev. 0x02)
pci1 at ppb0 bus 2
pci1: i/o space, memory space enabled, rd/line, wr/inv ok
isp0 at pci1 dev 0 function 0: QLogic 1020 Fast Wide SCSI HBA
isp0: interrupting at dec_1000a irq 0
isp0: invalid NVRAM header
tlp0 at pci1 dev 1 function 0: DECchip 21040 Ethernet, pass 2.4
dec_1000a_intr_map: can't map dev 8 pin 2
tlp0: unable to map interrupt
tlp1 at pci0 dev 11 function 0: DECchip 21140 Ethernet, pass 1.2
tlp1: interrupting at dec_1000a irq 1
tlp1: DEC DE500-XA, Ethernet address 00:00:f8:02:10:1c
tlp1: 10baseT, 100baseTX, 100baseTX-FDX, 10baseT-FDX
siop0 at pci0 dev 12 function 0: Symbios Logic 53c810 (fast scsi)
siop0: interrupting at dec_1000a irq 3
scsibus0 at siop0: 8 targets, 8 luns per target
siop1 at pci0 dev 13 function 0: Symbios Logic 53c810 (fast scsi)
siop1: interrupting at dec_1000a irq 5
scsibus1 at siop1: 8 targets, 8 luns per target
eisa0 at pceb0
eisa0: can't map I/O space for slot 9
isa0 at pceb0
lpt0 at isa0 port 0x3bc-0x3bf irq 7
com0 at isa0 port 0x3f8-0x3ff irq 4: ns16550a, working fifo
com1 at isa0 port 0x2f8-0x2ff irq 3: ns16550a, working fifo
pckbc0 at isa0 port 0x60-0x64
pckbd0 at pckbc0 (kbd slot)
pckbc0: using irq 1 for kbd slot
wskbd0 at pckbd0: console keyboard
pms0 at pckbc0 (aux slot)
pckbc0: using irq 12 for aux slot
wsmouse0 at pms0 mux 0
vga0 at isa0 port 0x3b0-0x3df iomem 0xa0000-0xbffff
wsdisplay0 at vga0 kbdmux 1: console (80x25, vt100 emulation), using  
wskbd0
wsmux1: connecting to wsdisplay0
pcppi0 at isa0 port 0x61
midi0 at pcppi0: PC speaker (CPU-intensive output)
spkr0 at pcppi0
isabeep0 at pcppi0
fdc0 at isa0 port 0x3f0-0x3f7 irq 6 drq 2
mcclock0 at isa0 port 0x70-0x71: mc146818 compatible time-of-day clock
timecounter: Timecounter "clockinterrupt" frequency 1024 Hz quality 0
timecounter: Timecounter "PCC" frequency 300007008 Hz quality 1000
scsibus0: waiting 2 seconds for devices to settle...
scsibus1: waiting 2 seconds for devices to settle...
scsibus2 at isp0: 16 targets, 8 luns per target
scsibus2: waiting 2 seconds for devices to settle...
IPsec: Initialized Security Association Processing.
fd0 at fdc0 drive 0: 1.44MB, 80 cyl, 2 head, 18 sec
sd0 at scsibus2 target 0 lun 0: <DEC, RZ29B    (C) DEC, 0016> disk fixed
sd0: async, 8-bit transfers
sd0: 4091 MB, 3708 cyl, 20 head, 113 sec, 512 bytes/sect x 8380080  
sectors
sd0: sync (100.00ns offset 12), 16-bit (20.000MB/s) transfers, tagged  
queueing
sd1 at scsibus2 target 1 lun 0: <IBM-PCCO, DDRS-39130W   !#, S97B>  
disk fixed
sd1: 8678 MB, 8387 cyl, 10 head, 211 sec, 512 bytes/sect x 17774160  
sectors
sd1: sync (100.00ns offset 12), 16-bit (20.000MB/s) transfers, tagged  
queueing
sd2 at scsibus2 target 3 lun 0: <DEC, RZ29B    (C) DEC, 0016> disk fixed
sd2: async, 8-bit transfers
sd2: 4091 MB, 3708 cyl, 20 head, 113 sec, 512 bytes/sect x 8380080  
sectors
sd2: sync (100.00ns offset 12), 16-bit (20.000MB/s) transfers, tagged  
queueing
cd0 at scsibus2 target 4 lun 0: <DEC, RRD45   (C) DEC, 0436> cdrom  
removable
cd0: async, 8-bit transfers
cd0: sync (248.00ns offset 12), 8-bit (4.032MB/s) transfers
sd3 at scsibus2 target 5 lun 0: <IBM OEM, DCHS04Z, 6161> disk fixed
sd3: 4340 MB, 6077 cyl, 9 head, 162 sec, 512 bytes/sect x 8888543  
sectors
sd3: sync (100.00ns offset 12), 8-bit (10.000MB/s) transfers, tagged  
queueing
Kernelized RAIDframe activated
raid0: RAID Level 1
raid0: Components: /dev/sd0a /dev/sd2a
raid0: Total Sectors: 262016 (127 MB)
raid1: RAID Level 1
raid1: Components: /dev/sd0b /dev/sd2b
raid1: Total Sectors: 524160 (255 MB)
raid2: RAID Level 1
raid2: Components: /dev/sd0d /dev/sd2d
raid2: Total Sectors: 3483008 (1700 MB)
raid3: RAID Level 5
raid3: Components: /dev/sd0e /dev/sd3a /dev/sd2e
raid3: Total Sectors: 8220800 (4014 MB)
root on raid0a dumps on raid0b
root file system type: ffs
=====>8=====

Does anyone else encounter this problem, or have any suggestions for  
fixing it?  The problem is inconvenient, rather than fatal--- 
inconvenient because I don't have ready physical access to the machine  
and so it makes remote updates requiring a reboot impossible, unlike  
before. :-(

Any help is gratefully appreciated.

Cheers,

Paul.