When modifying audio, make sure:
-Sampling rate / Project rate is the same as the original file (usually 22,050Hz for most weapons) *
-Track is in mono, not stereo
-Duration is roughly the same as the original file **
-Export as a 16 bit .WAV
* You can raise the sampling rate without bugs only if you decrease the sampling rate of other sounds in the same sound bank.
** If the new sound you're using is longer than the original audio file, you'll need to shorten other audio files in bank_137 to avoid bugs with other game sounds (such as rain and reloading).
Also, if you're using SAAT GUI Frontend, try the alternate method (using command prompt and temp folder) to see if that fixes the problem.