The peak in the signal may introduce high frequency components (> 2000Hz in your case). So when you apply a lowpass filter, it will be affected. The disstortion when the order is high is because of your signal is of finite length (You do not have all the history data of the signal). A less than 10 order should work for most of cases.
If you like, you may attach your signal and VI so that I can look at it in more details.
