Same problem here, very disturbing.
System will run fine at the beginning of my work. CPU usage is about 50-60%, Cubase VST meter shows around 75%, no spikes or crackles. I do live recordings of long durations. After some time into the recording, I get occasional spikes and crackles and their frequency does increase over time.
For me the symptoms first appeared 1 week ago when I started to test some Lexicon plugins which require Ilok authorization. I initially suspected that either the Ilok drivers or the plugins are the source of the problem. However, since I did upgrade from 6.0.5 to 6.5 at the same time, I cannot be sure.
When I would disable one of the plugins (i.e., Lexicon PCM Hall), the spikes would disappear instantly - but only for a while. Tried the same with removed plugin, and the spikes still happened, so it won't be the plugin.
Now I completeley removed Ilok drivers from my system and Ilok authorized plugins from the project to see whether it has anything to do with this phenomenon. I will report back middle of next week when I have new results.
SW: C 9.5 /64 & Wavelab 9 on W10/64
DAW 1: DA-X Extreme Haswell-E Xeon E5-2680V3 12-core workstation
DAW 2: Dell Precision T5500 2 x Xeon X5690 12-core workstation
Audio: 4 x rme HDSPe / Multiface II, 3 x Octamic II, 1 x rme Fireface UC
Surface: 3 x Avid MC Mix, 1 x MC Transport
Plugins: Audioease, Lexicon, Neve Portico, Yamaha Vintage, SlateDigital, Izotope, Pianoteq etc.