I am also using SWAT model and run this model many times with the examples provided with it. I did not have problems with it. I will recommend to you to run it again carefully and if still you have problems just update it here. I will also run it again and will be able to answer your problems. I hope it will work.
If you have measured weather data inputs, ensure they are prepared using correct format. share sample of weather data input files. just the first 5 for each (pcp, s, rh, w & t).