Dear Tomik,
Freescale MCUs with an Internal Clock Generator module (ICG) usually include a trimming capability.
The Internal RC oscillator can vary with fabrication process. The trimming allow users to get always the target frequency precisely.
Also usually, the programming tool do the trimming and store the trimming value in Flash.
However, usually again, the trim value is not loaded into REGISTER automatically after RESET.
So what probably occurs is that the ICG is trimmed and value adjusted when you Flash.
After pressing Reset you lose the TRIM and get a different reference clock which multiplied by the FLL/PLL, amplifies the difference.
Look in the datasheet for "TRIM" and usually (the last one for this post, I promise) you just need to write one line to load the value from FLASH to REGISTER.
Cheers,
Alban. {usually}