Boot system flash: does not appear on 2960 running config

Question

Dear friends,
On the 2960, i have two .bin images and i am pointing to the latest one.
However, the boot system flash: command along with the new image does not appear in the running config but it appears in the
show boot command.
t3a.sidradc.dmz.01#dir flash:
Directory of flash:/
    2  -rwx        2131   Jan 3 2010 07:30:45 +03:00  private-config.text
    4  -rwx     8040418   Mar 1 1993 05:31:51 +03:00  c2960-lanbasek9-mz.122-50.SE3.bin
    5  -rwx         676   Jan 3 2010 07:28:50 +03:00  vlan.dat
    6  drwx         128   Mar 1 1993 03:02:32 +03:00  c2960-lanbasek9-mz.122-44.SE6
  546  -rwx        4120   Jan 3 2010 07:30:45 +03:00  multiple-fs
  548  -rwx        9001   Jan 3 2010 07:30:45 +03:00  config.text
32514048 bytes total (21123072 bytes free)
t3a.sidradc.dmz.01(config)#boot system flash:c2960-lanbasek9-mz.122-50.SE3.bin
t3a.sidradc.dmz.01(config)#exit
t3a.sidradc.dmz.01#wr
Building configuration...
[OK]
t3a.sidradc.dmz.01#sh boot
BOOT path-list      : flash:c2960-lanbasek9-mz.122-50.SE3.bin
Config file         : flash:/config.text
Private Config file : flash:/private-config.text
Enable Break        : no
Manual Boot         : no
HELPER path-list    :
Auto upgrade        : yes
Auto upgrade path   :
NVRAM/Config file
      buffer size:   65536
Timeout for Config
          Download:    0 seconds
Config Download
       via DHCP:       disabled (next boot: disabled)
t3a.sidradc.dmz.01#sh run | inc boot
boot-start-marker
boot-end-marker
Are you aware of any reasons for this?
Thanks a lot
Gautam

Answer 1

and the other being the issue where IOS can return the prompt before it's done unpacking the files
Ok, now what EXACTLY is the appliance and IOS version?  The only time I know of this bug is the Metro Ethernet (ME) switches and when the current appliance is upgraded FROM an IOS version 15.2(1)S.  
But there is a "workaround" which Cisco doesn't want to publish (don't ask me why not):  Use "archive tar /x" and, optionally, delete the old IOS sub-directory.
Personally, I wouldn't recommend anyone using the "copy the BIN file" method unless you know what you are doing or you've put extra measures in place.  The "archive /x tar" and/or "archive download-sw" was developed so that it could be automated and the operator can see the result at the end.  The "copy the BIN file" method doesn't give anyone a result whether or not the file was copied or not or was the file copied completely.  
Regularly, I would upgrade our switches (2960/2960S, ME-3800X, 3560E/3560CG, 3750X) fleet using the "archive download-sw" method and I don't use scripts.  I just copy-and-paste the command.  So far, since 2009, I've "lost" only 6 switches when I upgraded the switch to upgrade the wrong file (another IOS bug on it's own) and I had to physically show up and upgrade using ROMmon.  Every time I would upgrade, about 900 switches (some in a stack), it would take me about 4 days.  Even though I work with three guys who's very good at almost any scripting but we've come to a unanimous conclusion NOT to use scripting.  
Moving on, if "copy the BIN file" is still a preferred choice, I would like to know how do you go about verifying the file was copied completely?  Whenever I resort to the "copy the BIN file", I ensure the file copied is complete by verifying the MD5 hash value against the MD5 hash value found in the Cisco website.  Trust me, adding this additional "layer" of security saved me doing ROMmon upgrade so many times.