This can be caused by several different things. Clicks like this are mainly caused by a large, instantaneous jump in value between consecutive samples. Going from zero while at idle to an offsetted value at punch-in would yield a click. After recording in Nuendo or Cubase, highlight the track and go to Audio > Process > Remove DC Offset.
Another solution is to enable Snapping to Zero Crossings. In Nuendo and Cubase SX, go to File > Preferences > Audio (under the Edit heading) > check the box next to “Snap to Zero Crossing.” In Cubase SE, File > Preferences > Audio is under the Editing heading. In Cubase LE, Snap to Zero is directly in File > Preferences > Audio.
The last resort is to draw in automation. Automating a short ramp down to zero dB at the start of the recorded file is an effective method of eliminating clicks and pops like these. In Nuendo, see Chapter 13 for help with automation. In Cubase SX, see Chapter 14. In Cubase SE, see Chapter 12. In Cubase LE, see Chapter 9.
*** All version referenced were the latest as of 4/4/06 (Nuendo 3.2.0 Build 1128; Cubase SX 3.1.1 Build 944; Cubase SE 3.0.2 Build 643; Cubase LE 1.0.8 Build 104) ***