I've done a lot of recording of tape to disk, and never had
the problems you mention.
Most often I use CoolEdit Pro, simply for the ease with which
I can clean out tape hiss or other noises once I'm done.
In other audio work, you can get clicks and/or crackling in
audio, particularly during recording, if audio buffer sizes
are too large for your system.
Check in your audio card settings and/or whatever program
your using to record, see if it allows for changing buffering
settings. If it does, lower it a notch or two, and those clicks
should go away. If you're using a recent model hard-drive,
just recording to that, in itself, shouldn't be causing your
problem.