Thanks for your help Will.
The problem isn't with burning a master from the original .wav files. THis all goes smooth and the master disc is as it should be, without any clicks. The problem is with the Kunaki software. This software imports the master CD and combines this with the artwork and release data. It creates an .exe & .pac file which should be checked before sending this package to the Kunaki facility. Once the waves has been exported you should listen to all audio as this is an excact copy of the one that will be burned to CD. All is good, no cracks in the audio but only a little click at the transfer while listening in Winamp for example. This didn't happen with the previous editions..
Once I burn the exported .wav files onto a new master it sounds good but when playing them in Winamp for instance, the clicks appears. I did this with the Kunaki master of OoT3, just to check if the little clicks were also present while playing them in Winamp.. but they didn't, so I guess the master isn't good. I'll now upload this master anyway and send a copy to turquiose70, he then will listen and check if it is ok.
Uploading the tracks to last.fm is also a no go atm.. because
this problem occurs :/