I've been having the same problem.  But only on one of my machines.  So, 
on a hunch, I quit thunderbird, deleted the global-messages-db.sqlite, 
relaunched thunderbird and let it reindex from scratch.  After some 
minutes, the indexing was finished and the cpu usage by thunderbird 
returned to zero.  Everything seems fine now.

Hope this might work for you??

I'm going to guess that there is some bug that promotes a race condition 
under rare circumstances, either on upgrade or otherwise.

On 04/30/2012 09:54 PM, Vex Mage wrote:
> To be clear. Mozilla's reindexing code causes "stupidly" high CPU usage
> and effects pretty much all Ubuntu users who upgrade Thunderbird and
> this period of unusable desktop experience is ok because it only happens
> once? I think Thunderbird should not make the assumption that it's the
> only app using the cpu. I disagree with categorizing this bug as
> invalid.
>

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You received this bug notification because you are a member of Desktop
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https://bugs.launchpad.net/bugs/984801

Title:
  Thunderbird 11 has stupidly high idle CPU usage

Status in “thunderbird” package in Ubuntu:
  Invalid

Bug description:
  Running Ubuntu 10.04 LTS 32-bit and today I got the upgrade from
  Thunderbird 3.6.X to 11.0.1 and noticed it is using a stupid amount of
  CPU time when apparently idle. On my quad-core AMD machine it is
  taking typically 30-50% CPU when doing nothing, and this is much the
  same when minimised, as shown by 'top'

  top - 12:50:00 up  1:59,  4 users,  load average: 1.27, 0.99, 1.03
  Tasks: 230 total,   3 running, 226 sleeping,   0 stopped,   1 zombie
  Cpu(s): 12.2%us,  1.4%sy,  0.0%ni, 82.5%id,  3.9%wa,  0.1%hi,  0.0%si,  0.0%st
  Mem:   2706608k total,  2621568k used,    85040k free,   148192k buffers
  Swap:        0k total,        0k used,        0k free,  1612160k cached

    PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND          
                                                                                
                   
  20049 paul      20   0  478m 157m  33m R   46  6.0   0:57.14 thunderbird-bin  
                                                                                
                   
  19759 paul      20   0  270m 195m  18m S    4  7.4   1:07.00 opera            
                                                                                
                   
   3918 paul      20   0  165m  24m  12m S    1  0.9   1:25.70 chromium-browse  
                                                                                
                   
  19215 paul      20   0  2652 1340  984 S    1  0.0   0:21.85 htop             
                                                                                
                   
   1317 root      20   0  152m  98m  13m S    1  3.7   8:20.29 Xorg             
                                                                                
                   
   4422 paul      20   0 49096  13m 9.8m S    0  0.5   1:22.72 gnome-terminal   
                                                                                
                   
  20165 paul      20   0  2544 1272  912 R    0  0.0   0:00.06 top              
                                                                                
                   
      1 root      20   0  2808 1664 1168 S    0  0.1   0:00.56 init             
                                                                                
                   
      2 root      20   0     0    0    0 S    0  0.0   0:00.00 kthreadd         
                                                                                
                   
      3 root      RT   0     0    0    0 S    0  0.0   0:00.11 migration/0  

  This is APPALLING for anyone on a laptop where power consumption (and
  hence battery life) is directly related to CPU use!

  What is Thunderbird doing with all of the CPU cycles?

  I tried running it in safe mode, and have already disabled any plugins
  but to no improvement. I also tried running it via strace and it spews
  out a lot of system calls even when idle, most oddly are blocks like
  this:

  clock_gettime(CLOCK_MONOTONIC, {6787, 22357603}) = 0
  clock_gettime(CLOCK_MONOTONIC, {6787, 22435200}) = 0
  gettimeofday({1334749406, 311330}, NULL) = 0
  gettimeofday({1334749406, 311537}, NULL) = 0
  gettimeofday({1334749406, 311670}, NULL) = 0
  futex(0xb75eb5c8, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0xb75eb5c4, {FUTEX_OP_SET, 0, 
FUTEX_OP_CMP_GT, 1}) = 1
  open("/home/paul/.thunderbird/3c38dt95.default/session.json", 
O_WRONLY|O_CREAT|O_TRUNC|O_LARGEFILE, 0664) = 56
  write(56, "{\"rev\":0,\"windows\":[{\"type\":\"3pa"..., 396) = 396
  close(56)                               = 0
  gettimeofday({1334749406, 314673}, NULL) = 0
  clock_gettime(CLOCK_MONOTONIC, {6787, 26165961}) = 0
  clock_gettime(CLOCK_MONOTONIC, {6787, 26256350}) = 0
  clock_gettime(CLOCK_MONOTONIC, {6787, 26329526}) = 0
  gettimeofday({1334749406, 315949}, NULL) = 0
  gettimeofday({1334749406, 316354}, NULL) = 0
  gettimeofday({1334749406, 316908}, NULL) = 0
  gettimeofday({1334749406, 317088}, NULL) = 0

  Notice it is calling gettimeofday() every 100us or so! Looks like
  someone should be using usleep() or similar time-wasting methods when
  nothing is happening :(

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