Observations with Pops, Clicks and various Plugs

I only use and have X1 Producer installed-Nothing else.
 
I can record hours of practice sessions, split the individual songs out by right clicking and Split and Fading in and out manually.
 
I noticed yesterday trying some new things out that everything I do manually doesnt produces these noises but if I take a clip and let Sonar split the clip at the transients, do cross fades, or whatever, its trouble with noises or performance.
 
Also Transient Shaper, Perfect Space and a few other X1 plugs do not like my system. I can use similar effects and not have problems.
 
Never had a need to go into these but thought I would try a few things out.
 
Ill stick with my old manual way until its worked out. No problem on this end
 
 

As for splitting clips at the transients I was just experimenting with some rough raw garage recordings trying things out with knocking out bleed/spillage and trying to tune up the drum kits. But just experimenting.

Not sure on the TS & PS (memory intensive plugs?). I figured my system should have been good enough to run it.  If I insert it in the FX bin, my other tracks will drop out intermittently (meaning the audio recording and wave is there, but sound might or might not play back in spots throughout the clips), midi tracks will be in and out, hit and miss on the notes playing back.

As for the Hard drives, I have one 1TB internal and a 500 GB external hard drive. I use the external to save the projects on and work from there but X1 is on the Internal with the operating system.

The PS & TS have been fine up until recently without any probs.  Havent changed anything and the computer is fairly clean as to what is on it and how much is stored. I think the only thing I have done recently is experimented with adding Session Drummer 3 tracks into the Audio Track projects which I havent done in the past. Usually all my projects are mic'd tracks.

Im thinking about getting an extra external hard drive but not sure on how to set-up or if it would benefit me to. 
    OS on computer
    X1 on Ext 1
    Projects  on Ext 2

???   is this kinda the norm for multiple drives?
 
ADDED  When everything is acting up, the hard drive status indicator and memory are hardly even being worked as indicated up in the Control Bar.
This is on projects with just 6 short audio tracks at about 3-4 minutes long.