I also have a similar problem - changing settings through the indicator on a dual core system only changes the freq of the first CPU. 

Here's the output of my /cat/proc/cpuinfo if i change the indicator to 2Ghz (for example):

processor	: 0
vendor_id	: GenuineIntel
cpu family	: 6
model		: 15
model name	: Intel(R) Core(TM)2 CPU         T7200  @ 2.00GHz
stepping	: 6
cpu MHz		: 2000.000
cache size	: 4096 KB
physical id	: 0
siblings	: 2
core id		: 0
cpu cores	: 2
apicid		: 0
initial apicid	: 0
fpu		: yes
fpu_exception	: yes
cpuid level	: 10
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm lahf_lm dts tpr_shadow
bogomips	: 3990.34
clflush size	: 64
cache_alignment	: 64
address sizes	: 36 bits physical, 48 bits virtual
power management:

processor	: 1
vendor_id	: GenuineIntel
cpu family	: 6
model		: 15
model name	: Intel(R) Core(TM)2 CPU         T7200  @ 2.00GHz
stepping	: 6
cpu MHz		: 1000.000
cache size	: 4096 KB
physical id	: 0
siblings	: 2
core id		: 1
cpu cores	: 2
apicid		: 1
initial apicid	: 1
fpu		: yes
fpu_exception	: yes
cpuid level	: 10
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm lahf_lm dts tpr_shadow
bogomips	: 3990.22
clflush size	: 64
cache_alignment	: 64
address sizes	: 36 bits physical, 48 bits virtual
power management:

and here is the output of cpufreq-info:

driver: acpi-cpufreq
  CPUs which run at the same hardware frequency: 0 1
  CPUs which need to have their frequency coordinated by software: 0
  maximum transition latency: 10.0 us.
  hardware limits: 1000 MHz - 2.00 GHz
  available frequency steps: 2.00 GHz, 1.67 GHz, 1.33 GHz, 1000 MHz
  available cpufreq governors: conservative, ondemand, userspace, powersave, performance
  current policy: frequency should be within 1000 MHz and 2.00 GHz.
                  The governor "ondemand" may decide which speed to use
                  within this range.
  current CPU frequency is 2.00 GHz.
  cpufreq stats: 2.00 GHz:1.51%, 1.67 GHz:0.07%, 1.33 GHz:0.09%, 1000 MHz:98.33%  (86493)
analyzing CPU 1:
  driver: acpi-cpufreq
  CPUs which run at the same hardware frequency: 0 1
  CPUs which need to have their frequency coordinated by software: 1
  maximum transition latency: 10.0 us.
  hardware limits: 1000 MHz - 2.00 GHz
  available frequency steps: 2.00 GHz, 1.67 GHz, 1.33 GHz, 1000 MHz
  available cpufreq governors: conservative, ondemand, userspace, powersave, performance
  current policy: frequency should be within 1000 MHz and 2.00 GHz.
                  The governor "ondemand" may decide which speed to use
                  within this range.
  current CPU frequency is 1000 MHz.
  cpufreq stats: 2.00 GHz:0.17%, 1.67 GHz:0.00%, 1.33 GHz:0.00%, 1000 MHz:99.83%  (113)

It would be easier if the indicator could use one setting for both CPUs (perhaps offer a checkbox/setting "Use same frequence on all CPUs")...

I hope you have time to work on this, I'm loving the indicator.