Hello Colin,
I don't know if you has fixed your problem with the clicks & pops, and the worst positioning of the notes, when you playback Logic after have recorded something...but you can be sure I was have the EXACTLY SAME PROBLEM, but with the Cubase SX (version 2, the SX3 has a different trick!).
I apologize for my English, but I need to explain you exactly, what is my setup in the studio, and so, you can make an idea to comparing with your rig, because I am sure you'll fix the nightmare...I was working with customers inside the control room, watching the movie with my composition to see the development, ambience, etc, and just in the "right moment"...click,clack, pop...so lets go.
My basic system is a SONY DMX R100, radar 24, and PC pentium IV 3000 mhz, 1,5 gb RAM, 128 Mb graphics card, 120GB internal hdd+ 200GB external hd (just for gigastudio,VSL,etc)USB 2.0.
I have the SONY and the RADAR 24 connected via AES-EBU with 24 ch in/out, and the MARIAN MARC X card inside of PC,connected via ADAT TOS link 8 ch to the SONY; all working at 48 khz/24bits and th e wordclock connections of that way: PC generate master wordclock signal to RADAR 24, and the last one to SONY.( I never wanted this setup, but I can do it of another way ,because the gigastudio it don't be run...).
You know, I am sure, than if you have some mistake about the right order when you start your rig you should do it with "the system wants", in my case
first I start the PC, I load the GIGA project, after a right load, inside him, I open cubase , and if all goes find, I power on the Radar, and finally, the SONY, (believe me, if I don't do it exactly how you are reading it, I will have bad sync with wordclock !!
I explain you this, because the problem than you have is VERY,VERY close about the noises I have mentioned, but these noises (the mine)are constant, sometimes it looks like a "digital broken metronome"...BUT these are a common wordclock problem (worse or deficient conections). IT'S NOT YOUR PROBLEM!!! (I wanted to explain the differences between both possible causes). lets go streigth to the another "kind " of noises, the noises than you ear...
A lot of years ago, a drivers created by Microsoft to ensure the right compatibility, more or less, with the new sound cards from those years
(90's)was introduced in every computer with Windows OS, but not with a bad idea, from a silent way, it does'n matter so much...these drivers were called "EMULATED MIDI PORT"; these drivers are "living"near to the native drivers of your sound card, and when I opened a lot of times the "device controller" of my cubase, I always saw them...and curiosity ,if you have a M-audio card, you will see too "emulated M-audio midicard " or somethig like that with the same name of your card , but you can`t choose an option that says only the name of your native driver ,dry. If all of this, it's close to
some of your feelings...here comes the solution what worked well to me at last...
I don't know the Mac's (I want to have one) but you should check all I gonna tell you, because even are different OS, it must be the same problem...Inside the main CUBASE SX directory, there's a folder called "midiportfile", and inside himself, there's a single file called with the same name "midiportfile", ok. Move this single file outside of the "midiportfile" folder, no erase nothing, and paste it in the main directory of the program (cubase, logic, whatever)so you will have an empty folder, but it must to stay so...empty, ok?
Now you reset the computer, and you go back again inside the "device configurator", and check if you see the "emulated drivers" or not, but surely you will see the native drivers of your sound card dry, select all your tracks with the right and "new" midi in/out drivers , play something, record it, and AFTER 15 or 20 minutes,( I always did have problems after this time, more or less)NOT BEFORE, and if you will see than your music plays perfectly adjusted to your click, or synchronized to another machine, they goes fine...voilà!!. Look, I was working with a single sound of the Vienna symphonic library, an EH_ensemble_horn OF 24 BITS, and the CPU indicator becomes red, and the clicks were terrible, but I knew I have an enough power to run 2 programs with a lot of instruments inside (with limits of coarse)but with a single instrument, without reverb, makes the CPU's full loading?...
Actually, I am working on ambients, and looking for the characters of how the music must sounds, and I have 21 heavy instruments loaded on gigastudio 3, with a pair of Absynts 3 on CUBASE SX, some audio reference tracks, a video track with an mpeg reference file, two keyboards attached to Marian both to real midi time performance, and it's not enough, I have a Wave IR-1 convolution reverb at the master bus...and works better than great!!!!no problems with "my" loved noises, no problem about midi in/out...only if I put some track more of VSL percussion, the CPU'S rises sometimes...the red bar, but very few times, so I am happy now.
I hope this "option" can help you, but one is PC, and the other is a Mac and I don't know nothing about Mac.
Good Luck
Xavier Duch
Wildsoun studios
Barcelona