Why FSK demodulator output different bitstreams in case of the same inputs of different lengths?

Hi everyone,
   Recently I was trying to do FSK demodulation with Labview and my USRP2.
   I did the following two tests, but found a strange phenomenon:
   In the first test, I use the demodulator to demodulate a waveform of 18399 samples, where the signal occupies about the first 12000 samples, and the FSK demodulator outputs a bitsream of 1116 bits.
   The input waveform is shown in the following figure.
   In the second test, I use the demodulator to just demodulate the first 12000 samples of the waveform,  and I found that the demodulator outputs a bitstream of 705 bits.
  The input waveform is shown in the following figure:
   According to my understanding, as the input of the 2nd test  is the same as the first part of the first 1st test, the output bitstream of the 2st test must be equal to the output of the 1st test. However, they looks very different. In the first test, even the sync  sequence of bits cannot be found. 
    Can any one  help me explain why?  Thanks in advance!  
   In the attachment, I post the program and my test data.
Attachments:
questions.zip ‏506 KB

Hello Anthony F,
   Yes, I use the modulation toolkit.But I encapulate it into a subvi. Sorry for that I forget to attach it.
Attachments:
sub_demodulate_FSK_data.vi ‏21 KB

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